5VCY - chain A (model A) | Protein kinase, membrane associated tyrosine/threonine 1
Structure information
PDB:5VCY
PubMed:28792760
Release date:2017-08-23
Resolution:1.56 Å
 
Kinase:PKMYT1 (MYT1)
Family:WEE
Group:Other
Species:HUMAN
 
Quality Score:8
Missing Residues:0
Missing Atoms:0
DFG conformation:in
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:Yes (2.7Å)
 
 
ASP rotation (xDFG.81) :330°
PHE rotation (xDFG.82) :357°
Activation loop position:-3.3Å
αC-helix position:18.5Å
 
G-rich loop angle:57.7°
G-rich loop distance:17.8Å
G-rich loop rotation:54°
Other models from this PDB:
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I2
H-bond protein
I4
H-bond protein
I5
H-bond ligand
H-bond protein
Binding pocket sequence
UniprotSRLGHGSYGEVFKYAVKRSRKLAEVGSHEKVGPCCVRLEQAYLQTELC-GPSLQQHCEAHLHSQGLVHLDVKPANIFLLGDFGLL
Structure:SRLGHGSYGEVFKYAVKRSRKLAEVGSHEKVGPCCVRLEQAYLQTELC_GPSLQQHCEAHLHSQGLVHLDVKPANIFLLGDFGLL


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: DB8
Ligand Name: 4-[(2,4-dichloro-5-methoxyphenyl)amino]-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinoline-3-carbonitrile

  • Download image
  • LABELS
  • KLIFS residue #
  • Amino Acid
  • None
  • COLORS
  • Interaction types
  • KLIFS (all res.)
  • KLIFS (interacting res.)
  • None
  • OTHER
  • Show/hide non-interacting res.
  • En/disable resizing interacting res.
This ligand targets the following (sub)pockets:
Main pockets
Front

Gate

Back

Subpockets
FP-I

FP-II

BP-I-A

BP-I-B

BP-II-in

BP-II-A-in

BP-II-B-in

BP-II-out

BP-II-B

BP-III

BP-IV

BP-V

Kinase-ligand interactions
Hydrophobic Aromatic face-to-face Aromatic face-to-edge H-bond donor H-bond acceptor Ionic positive Ionic negative
I g.l II III αC
1 S
114
2 R
115
3 L
116
4 G
117
5 H
118
6 G
119
7 S
120
8 Y
121
9 G
122
10 E
123
11 V
124
12 F
125
13 K
126
14 Y
136
15 A
137
16 V
138
17 K
139
18 R
140
19 S
141
20 R
153
αC b.l IV
21 K
154
22 L
155
23 A
156
24 E
157
25 V
158
26 G
159
27 S
160
28 H
161
29 E
162
30 K
163
31 V
164
32 G
165
33 P
168
34 C
169
35 C
170
36 V
171
37 R
172
38 L
173
39 E
174
40 Q
175
IV V GK hinge linker αD αE
41 A
176
42 Y
184
43 L
185
44 Q
186
45 T
187
46 E
188
47 L
189
48 C
190
49 _
_
50 G
191
51 P
192
52 S
193
53 L
194
54 Q
195
55 Q
196
56 H
197
57 C
198
58 E
199
59 A
200
60 H
223
αE VI c.l VII VIII x
61 L
224
62 H
225
63 S
226
64 Q
227
65 G
228
66 L
229
67 V
230
68 H
231
69 L
232
70 D
233
71 V
234
72 K
235
73 P
236
74 A
237
75 N
238
76 I
239
77 F
240
78 L
241
79 L
249
80 G
250
DFG a.l
81 D
251
82 F
252
83 G
253
84 L
254
85 L
255

Interaction pattern search
Search KLIFS for kinase-ligand complexes with similar interaction patterns:
Specify the minimum similarity (0.00 no similarity, 1.00 identical)
Binding affinities
ChEMBL ID:CHEMBL288441
Bioaffinities: 409 records for 200 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensAdaptor-associated kinase5.65.65.8pKd2
Homo sapiensALK tyrosine kinase receptor6.26.26.2pKd1
Homo sapiensAMP-activated protein kinase, alpha-1 subunit5.45.45.4pKd1
Homo sapiensAnkyrin repeat and protein kinase domain-containing protein 15.75.75.7pKd1
Homo sapiensBMP-2-inducible protein kinase6.16.16.5pKd2
Homo sapiensBone morphogenetic protein receptor type-26.26.26.2pKd1
Homo sapiensBreakpoint cluster region protein8.58.58.5pKd2
Homo sapiensCaM kinase I delta777pIC501
Homo sapiensCaM kinase I delta6.36.36.3pKd1
Homo sapiensCaM kinase II alpha5.45.45.4pKd1
Homo sapiensCaM kinase II gamma6.76.76.7pIC501
Homo sapiensCaM kinase II gamma5.45.45.4pKd1
Homo sapiensCaM-kinase kinase beta6.16.16.1pKd1
Homo sapiensCasein kinase I alpha6.66.66.6pKd1
Homo sapiensCasein kinase I delta5.55.56.6pKd2
Homo sapiensCasein kinase I epsilon777pKd1
Homo sapiensCasein kinase I isoform alpha-like5.65.65.6pKd1
Homo sapiensCitron Rho-interacting kinase5.65.65.6pKd1
Homo sapiensCyclin-dependent kinase 75.95.95.9pKd1
Homo sapiensDiscoidin domain-containing receptor 26.96.96.9pKd1
Homo sapiensDual serine/threonine and tyrosine protein kinase6.46.46.4pKd1
Homo sapiensDual specificity mitogen-activated protein kinase kinase 1999pIC501
Homo sapiensDual specificity mitogen-activated protein kinase kinase 15.45.47.7pKd2
Homo sapiensDual specificity mitogen-activated protein kinase kinase 25.95.98pKd2
Homo sapiensDual specificity mitogen-activated protein kinase kinase 35.65.65.6pKd1
Homo sapiensDual specificity mitogen-activated protein kinase kinase 45.65.65.6pKd1
Homo sapiensDual specificity mitogen-activated protein kinase kinase 55.85.88.1pKd2
Homo sapiensDual specificity mitogen-activated protein kinase kinase 65.95.95.9pKd1
Homo sapiensDual specificity mitogen-activated protein kinase kinase 75.35.35.3pKd1
Homo sapiensDual specificity protein kinase CLK25.85.85.8pKd2
Homo sapiensDual specificity protein kinase CLK36.56.56.5pKd2
Homo sapiensDual specificity protein kinase CLK45.55.55.5pKd1
Homo sapiensDual specificty protein kinase CLK16.26.26.2pKd3
Homo sapiensEphrin type-A receptor 15.65.65.6pKd1
Homo sapiensEphrin type-A receptor 26.96.97.8pKd2
Homo sapiensEphrin type-A receptor 38.28.28.2pKd1
Homo sapiensEphrin type-A receptor 47.27.27.8pKd2
Homo sapiensEphrin type-A receptor 57.67.67.6pKd1
Homo sapiensEphrin type-A receptor 6666pKd1
Homo sapiensEphrin type-A receptor 88.18.18.1pKd1
Homo sapiensEphrin type-B receptor 17.57.57.5pKd1
Homo sapiensEphrin type-B receptor 28.18.18.1pIC501
Homo sapiensEphrin type-B receptor 26.66.68.1pKd2
Homo sapiensEphrin type-B receptor 35.85.86.7pKd2
Homo sapiensEphrin type-B receptor 48.38.38.3pIC501
Homo sapiensEphrin type-B receptor 4778pKd2
Homo sapiensEphrin type-B receptor 65.55.55.5pKd1
Homo sapiensEpidermal growth factor receptor erbB16.36.37.3pIC502
Homo sapiensEpidermal growth factor receptor erbB17.56.47.8pKd13
Homo sapiensEpithelial discoidin domain-containing receptor 16.96.96.9pKd1
Homo sapiensEukaryotic translation initiation factor 2-alpha kinase 16.26.26.2pKd1
Homo sapiensEukaryotic translation initiation factor 2-alpha kinase 46.66.66.6pKd1
Homo sapiensFocal adhesion kinase 16.36.36.3pIC501
Homo sapiensFocal adhesion kinase 16.26.26.2pKd2
Homo sapiensG protein-coupled receptor kinase 45.35.35.3pKd1
Homo sapiensG protein-coupled receptor kinase 75.85.85.8pKd1
Homo sapiensHepatocyte growth factor receptor5.55.25.7pKd3
Homo sapiensHomeodomain-interacting protein kinase 16.36.36.3pKd1
Homo sapiensHomeodomain-interacting protein kinase 25.75.75.7pKd1
Homo sapiensHomeodomain-interacting protein kinase 35.55.55.5pKd1
Homo sapiensHomeodomain-interacting protein kinase 46.96.96.9pKd1
Homo sapiensHormonally up-regulated neu tumor-associated kinase5.35.35.3pKd1
Homo sapiensInhibitor of nuclear factor kappa B kinase epsilon subunit6.16.17.3pKd2
Homo sapiensInterleukin-1 receptor-associated kinase 16.26.26.2pKd1
Homo sapiensInterleukin-1 receptor-associated kinase 46.26.26.2pIC501
Homo sapiensInterleukin-1 receptor-associated kinase 46.46.46.4pKd1
Homo sapiensLeucine-rich repeat serine/threonine-protein kinase 26.16.16.3pKd2
Homo sapiensLeukocyte tyrosine kinase receptor5.55.55.5pKd1
Homo sapiensMacrophage colony stimulating factor receptor6.46.46.4pKd1
Homo sapiensMacrophage-stimulating protein receptor5.25.25.2pKd1
Homo sapiensMicrotubule-associated serine/threonine-protein kinase 16.56.56.5pKd1
Homo sapiensMisshapen-like kinase 17.77.77.7pIC501
Homo sapiensMisshapen-like kinase 18.58.58.5pKd1
Homo sapiensMitogen-activated protein kinase 75.65.65.6pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase 15.45.47pKd2
Homo sapiensMitogen-activated protein kinase kinase kinase 115.65.65.6pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase 126.26.26.2pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase 136.36.36.3pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase 26.26.27.5pKd2
Homo sapiensMitogen-activated protein kinase kinase kinase 35.95.97.3pKd2
Homo sapiensMitogen-activated protein kinase kinase kinase 45.85.87pKd2
Homo sapiensMitogen-activated protein kinase kinase kinase 7777pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase 95.65.65.6pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 16.16.17.8pKd2
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 2888pIC501
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 27.17.18.5pKd2
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 37.27.28.3pKd2
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 48.18.18.1pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 59.59.59.5pIC501
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 57.87.89.3pKd2
Homo sapiensMixed lineage kinase 75.95.97.1pKd2
Homo sapiensMyosin IIIA5.25.25.2pKd1
Homo sapiensMyosin-IIIB5.65.65.6pKd1
Homo sapiensMyosin light chain kinase, smooth muscle6.36.36.3pKd1
Homo sapiensMyotonin-protein kinase777pKd1
Homo sapiensNerve growth factor receptor Trk-A7.77.77.7pIC501
Homo sapiensNerve growth factor receptor Trk-A5.55.55.5pKd1
Homo sapiensNeurotrophic tyrosine kinase receptor type 27.67.67.6pIC501
Homo sapiensNeurotrophic tyrosine kinase receptor type 25.95.95.9pKd1
Homo sapiensNT-3 growth factor receptor5.55.55.5pKd1
Homo sapiensNUAK family SNF1-like kinase 15.25.25.2pKd1
Homo sapiensNUAK family SNF1-like kinase 26.76.76.7pKd1
Homo sapiensPeripheral plasma membrane protein CASK6.16.16.1pKd1
Homo sapiensPhosphatidylinositol-4-phosphate 5-kinase type-1 alpha5.55.55.5pKd1
Homo sapiensPhosphorylase kinase gamma subunit 16.56.56.5pKd1
Homo sapiensPhosphorylase kinase gamma subunit 25.95.95.9pKd1
Homo sapiensPlatelet-derived growth factor receptor alpha5.35.35.3pKd1
Homo sapiensPlatelet-derived growth factor receptor beta5.65.66.7pKd2
Homo sapiensProtein kinase C delta5.85.85.8pKd1
Homo sapiensProtein kinase C epsilon5.65.65.6pKd1
Homo sapiensProtein kinase C nu5.35.35.3pKd1
Homo sapiensProtein kinase C theta666pKd1
Homo sapiensProtein kinase N15.55.55.5pKd1
Homo sapiensProtein kinase N25.55.55.5pKd1
Homo sapiensProtein tyrosine kinase 2 beta6.96.96.9pIC501
Homo sapiensProtein tyrosine kinase 2 beta6.46.46.4pKd1
Homo sapiensProto-oncogene tyrosine-protein kinase MER777pKd1
Homo sapiensReceptor protein-tyrosine kinase erbB-25.65.65.6pIC501
Homo sapiensReceptor protein-tyrosine kinase erbB-25.65.65.6pKd1
Homo sapiensReceptor protein-tyrosine kinase erbB-47.67.67.6pKd1
Homo sapiensReceptor tyrosine-protein kinase erbB-39.19.19.1pKd1
Homo sapiensRho-associated protein kinase 16.16.16.1pKd1
Homo sapiensRho-associated protein kinase 26.46.46.4pKd1
Homo sapiensRibosomal protein S6 kinase 16.26.26.2pKd1
Homo sapiensRibosomal protein S6 kinase alpha 25.55.55.5pKd2
Homo sapiensRibosomal protein S6 kinase alpha 35.95.95.9pKd2
Homo sapiensRibosomal protein S6 kinase alpha 65.65.65.6pKd2
Homo sapiensSerine/threonine-protein kinase 107.37.37.3pIC501
Homo sapiensSerine/threonine-protein kinase 106.16.18.2pKd2
Homo sapiensSerine/threonine-protein kinase 26.16.18.3pKd2
Homo sapiensSerine/threonine-protein kinase 248.48.48.4pIC501
Homo sapiensSerine/threonine-protein kinase 246.46.47.6pKd2
Homo sapiensSerine/threonine-protein kinase 256.16.16.1pKd1
Homo sapiensSerine/threonine-protein kinase 32A5.85.85.8pKd1
Homo sapiensSerine/threonine-protein kinase 337.47.47.4pKd1
Homo sapiensSerine/threonine-protein kinase 358.78.78.7pKd1
Homo sapiensSerine/threonine-protein kinase 366.26.26.2pKd1
Homo sapiensSerine/threonine-protein kinase Chk15.55.55.5pKd1
Homo sapiensSerine/threonine-protein kinase Chk26.96.96.9pKd1
Homo sapiensSerine/threonine-protein kinase DCLK35.35.35.3pKd1
Homo sapiensSerine/threonine-protein kinase GAK8.97.48.9pKd3
Homo sapiensSerine/threonine-protein kinase MST16.76.76.7pIC501
Homo sapiensSerine/threonine-protein kinase MST16.76.76.7pKd1
Homo sapiensSerine/threonine-protein kinase MST26.46.46.4pKd1
Homo sapiensSerine/threonine-protein kinase MST47.47.47.4pKd1
Homo sapiensSerine/threonine-protein kinase Nek116.26.26.2pKd1
Homo sapiensSerine/threonine-protein kinase NEK25.85.85.8pKd1
Homo sapiensSerine/threonine-protein kinase NIM15.85.85.8pKd1
Homo sapiensSerine/threonine protein kinase NLK5.75.75.7pKd1
Homo sapiensSerine/threonine-protein kinase PAK 15.65.65.6pKd1
Homo sapiensSerine/threonine-protein kinase PAK 25.75.75.7pKd1
Homo sapiensSerine/threonine-protein kinase PAK 35.25.25.2pKd1
Homo sapiensSerine/threonine-protein kinase PCTAIRE-15.65.65.6pKd1
Homo sapiensSerine/threonine-protein kinase PFTAIRE-15.95.95.9pKd1
Homo sapiensSerine/threonine-protein kinase PFTAIRE-25.85.85.8pKd1
Mycobacterium tuberculosisSerine/threonine-protein kinase pknB5.35.35.3pKd1
Homo sapiensSerine/threonine-protein kinase PLK15.85.85.8pKd1
Homo sapiensSerine/threonine-protein kinase PLK2666pKd1
Homo sapiensSerine/threonine-protein kinase RIO15.75.75.7pKd1
Homo sapiensSerine/threonine-protein kinase RIO35.85.85.8pKd1
Homo sapiensSerine/threonine-protein kinase RIPK25.45.45.4pKd1
Homo sapiensSerine/threonine-protein kinase SIK17.57.57.5pKd1
Homo sapiensSerine/threonine-protein kinase SIK26.76.77.5pKd2
Homo sapiensSerine/threonine-protein kinase SIK36.86.87.2pKd2
Homo sapiensSerine/threonine-protein kinase SRPK35.45.45.4pKd1
Homo sapiensSerine/threonine-protein kinase TAO15.95.95.9pKd1
Homo sapiensSerine/threonine-protein kinase TAO25.75.75.7pKd1
Homo sapiensSerine/threonine-protein kinase TAO36.56.56.5pKd1
Homo sapiensSerine/threonine-protein kinase TBK16.36.36.3pIC501
Homo sapiensSerine/threonine-protein kinase TBK1666.6pKd2
Homo sapiensSerine/threonine-protein kinase TNNI3K6.86.86.8pKd1
Homo sapiensSerine/threonine-protein kinase tousled-like 16.26.26.2pKd1
Homo sapiensSerine/threonine-protein kinase tousled-like 25.75.75.7pKd1
Homo sapiensSerine/threonine-protein kinase ULK15.95.95.9pKd1
Homo sapiensSerine/threonine-protein kinase ULK26.46.46.4pKd1
Homo sapiensSerine/threonine-protein kinase ULK36.36.36.3pKd1
Homo sapiensSerine/threonine-protein kinase VRK26.26.26.2pKd1
Homo sapiensSerine/threonine-protein kinase WEE16.35.77.1pKd3
Homo sapiensSPS1/STE20-related protein kinase YSK47.87.87.8pKd1
Homo sapiensSTE20/SPS1-related proline-alanine-rich protein kinase5.45.45.4pKd1
Homo sapiensStem cell growth factor receptor6.75.27.5pIC505
Homo sapiensStem cell growth factor receptor6.66.37.1pKd7
Homo sapiensTestis-specific serine/threonine-protein kinase 15.35.35.3pKd1
Homo sapiensTRAF2- and NCK-interacting kinase7.57.57.6pKd2
Homo sapiensTyrosine- and threonine-specific cdc2-inhibitory kinase6.26.26.9pIC504
Homo sapiensTyrosine- and threonine-specific cdc2-inhibitory kinase6.56.16.6pKd3
Homo sapiensTyrosine- and threonine-specific cdc2-inhibitory kinase6.56.57.9pKi5
Homo sapiensTyrosine kinase non-receptor protein 28.68.68.6pIC502
Homo sapiensTyrosine kinase non-receptor protein 26.96.97.5pKd2
Homo sapiensTyrosine-protein kinase ABL96.39.3pIC506
Homo sapiensTyrosine-protein kinase ABL10.17.710.5pKd17
Homo sapiensTyrosine-protein kinase ABL29.39.39.3pIC501
Homo sapiensTyrosine-protein kinase ABL27.77.78.8pKd2
Homo sapiensTyrosine-protein kinase BLK8.58.58.5pKd1
Mus musculusTyrosine-protein kinase BLK8.18.18.1pIC501
Homo sapiensTyrosine-protein kinase BMX8.18.19pIC502
Homo sapiensTyrosine-protein kinase BMX6.76.76.7pKd1
Homo sapiensTyrosine-protein kinase BTK8.68.68.6pIC501
Homo sapiensTyrosine-protein kinase BTK7.67.68.3pKd2
Homo sapiensTyrosine-protein kinase CSK7.27.27.2pIC501
Homo sapiensTyrosine-protein kinase CSK6.76.77.5pKd2
Homo sapiensTyrosine-protein kinase CTK5.25.25.2pKd1
Homo sapiensTyrosine-protein kinase FER6.36.36.3pIC501
Homo sapiensTyrosine-protein kinase FER6.16.16.4pKd2
Homo sapiensTyrosine-protein kinase FES6.56.56.5pIC501
Homo sapiensTyrosine-protein kinase FES6.56.56.5pKd1
Homo sapiensTyrosine-protein kinase FGR999pIC501
Homo sapiensTyrosine-protein kinase FGR8.28.28.2pKd1
Homo sapiensTyrosine-protein kinase FRK8.78.78.7pIC501
Homo sapiensTyrosine-protein kinase FRK7.67.68.9pKd2
Homo sapiensTyrosine-protein kinase FYN6.46.48.7pIC503
Homo sapiensTyrosine-protein kinase FYN6.86.88pKd2
Homo sapiensTyrosine-protein kinase HCK8.58.58.5pIC501
Homo sapiensTyrosine-protein kinase HCK8.56.98.5pKd3
Homo sapiensTyrosine-protein kinase ITK/TSK5.85.85.8pKd1
Homo sapiensTyrosine-protein kinase JAK2666pKd2
Homo sapiensTyrosine-protein kinase JAK35.95.95.9pKd2
Homo sapiensTyrosine-protein kinase LCK8.98.98.9pIC501
Homo sapiensTyrosine-protein kinase LCK7.57.59.2pKd2
Homo sapiensTyrosine-protein kinase Lyn8.18.18.1pIC502
Homo sapiensTyrosine-protein kinase Lyn7.27.28.4pKd2
Homo sapiensTyrosine-protein kinase receptor FLT35.75.56pKd7
Homo sapiensTyrosine-protein kinase receptor RET5.45.35.4pKd3
Homo sapiensTyrosine-protein kinase receptor Tie-15.55.55.5pKd1
Homo sapiensTyrosine-protein kinase receptor TYRO37.27.27.2pKd1
Homo sapiensTyrosine-protein kinase receptor UFO6.36.36.8pIC504
Homo sapiensTyrosine-protein kinase receptor UFO7.37.37.3pKd1
Homo sapiensTyrosine-protein kinase SRC8.479pIC5032
Homo sapiensTyrosine-protein kinase SRC96.89pKd4
Homo sapiensTyrosine-protein kinase Srms777pKd1
Homo sapiensTyrosine-protein kinase SYK7.37.37.3pIC501
Homo sapiensTyrosine-protein kinase SYK6.56.56.5pKd1
Homo sapiensTyrosine-protein kinase TEC6.66.66.6pIC501
Homo sapiensTyrosine-protein kinase TEC5.55.55.5pKd1
Homo sapiensTyrosine-protein kinase TIE-25.95.95.9pIC501
Homo sapiensTyrosine-protein kinase TIE-25.45.45.4pKd1
Homo sapiensTyrosine-protein kinase TXK7.47.47.4pIC501
Homo sapiensTyrosine-protein kinase TXK7.17.17.1pKd1
Homo sapiensTyrosine-protein kinase TYK25.25.25.4pKd4
Homo sapiensTyrosine-protein kinase YES9.49.49.4pIC501
Homo sapiensTyrosine-protein kinase YES6.86.88.4pKd2
Homo sapiensTyrosine-protein kinase ZAP-705.85.85.8pKd1
Homo sapiensWee1-like protein kinase 2777pKd2