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  5VCW - chain B | Protein kinase, membrane associated tyrosine/threonine 1
Structure information
PDB:5VCW
PubMed:28792760
Release date:2017-08-23
Resolution:2.25 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 (3.8Å)
 
 
ASP rotation (xDFG.81) :343°
PHE rotation (xDFG.82) :355°
Activation loop position:-3.1Å
αC-helix position:18.6Å
 
G-rich loop angle:61.6°
G-rich loop distance:18.9Å
G-rich loop rotation:49.6°
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: 93J
Ligand Name: (2E)-N-{4-[(3-chloro-4-fluorophenyl)amino]-3-cyano-7-ethoxyquinolin-6-yl}-4-(dimethylamino)but-2-enamide

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  • LABELS
  • KLIFS residue #
  • Amino Acid
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  • COLORS
  • Interaction types
  • KLIFS (all res.)
  • KLIFS (interacting res.)
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  • OTHER
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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:CHEMBL607707
Bioaffinities: 225 records for 107 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensAdaptor-associated kinase5.55.55.6pKd2
Homo sapiensALK tyrosine kinase receptor5.25.25.2pKd1
Homo sapiensBMP-2-inducible protein kinase5.75.66.3pKd3
Homo sapiensBreakpoint cluster region protein5.95.95.9pKd2
Homo sapiensCaM kinase I delta5.25.25.4pKd2
Homo sapiensCaM-kinase kinase alpha5.35.35.3pKd1
Homo sapiensCaM-kinase kinase beta5.75.65.9pKd3
Homo sapiensCasein kinase I delta5.45.46pKd2
Homo sapiensCasein kinase I epsilon75.87pKd3
Homo sapiensCasein kinase I isoform alpha-like666pKd1
Homo sapiensCitron Rho-interacting kinase6.56.56.5pKd1
Homo sapiensDeath-associated protein kinase 35.45.45.6pKd2
Homo sapiensDual specificity mitogen-activated protein kinase kinase 15.15.16.4pKd2
Homo sapiensDual specificity mitogen-activated protein kinase kinase 25.65.66.1pKd2
Homo sapiensDual specificity protein kinase CLK25.85.86.2pKd2
Homo sapiensDual specificity protein kinase CLK35.35.35.7pKd2
Homo sapiensDual specificity protein kinase CLK45.45.45.5pKd2
Homo sapiensDual specificity tyrosine-phosphorylation-regulated kinase 1B5.45.45.4pKd1
Homo sapiensDual specificty protein kinase CLK15.55.56pKd2
Homo sapiensEphrin type-A receptor 35.45.45.4pKd2
Homo sapiensEphrin type-A receptor 56.26.26.2pKd1
Homo sapiensEphrin type-A receptor 65.45.45.4pKd1
Homo sapiensEphrin type-A receptor 85.55.56.4pKd2
Homo sapiensEphrin type-B receptor 15.45.45.4pKd1
Homo sapiensEphrin type-B receptor 45.65.65.9pKd2
Homo sapiensEpidermal growth factor receptor erbB17.44.19.6pIC5018
Homo sapiensEpidermal growth factor receptor erbB19.47.99.6pKd12
Homo sapiensEukaryotic translation initiation factor 2-alpha kinase 46.56.56.5pKd1
Homo sapiensFocal adhesion kinase 15.45.45.4pKd1
Homo sapiensHepatocyte growth factor receptor5.25.25.2pKd1
Homo sapiensInterferon-induced, double-stranded RNA-activated protein kinase5.75.75.7pKd1
Homo sapiensMacrophage colony stimulating factor receptor5.45.45.4pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase 1777pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase 35.75.75.7pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase 46.66.46.9pKd3
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 1666.6pKd2
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 25.65.65.6pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 36.76.76.8pKd2
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 46.56.56.5pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 587.48.4pKd3
Homo sapiensMixed lineage kinase 75.95.96.1pKd2
Homo sapiensmyosin light chain kinase 25.45.45.8pKd2
Homo sapiensMyotonin-protein kinase7.27.27.2pKd1
Homo sapiensNUAK family SNF1-like kinase 25.65.65.6pKd1
Homo sapiensPhosphatidylinositol-5-phosphate 4-kinase type-2 beta5.65.65.6pKd1
Homo sapiensPhosphorylase kinase gamma subunit 15.55.55.8pKd2
Homo sapiensPhosphorylase kinase gamma subunit 25.65.65.6pKd1
Homo sapiensProtein kinase C delta5.35.35.3pKd1
Homo sapiensProto-oncogene tyrosine-protein kinase MER5.95.95.9pKd1
Homo sapiensReceptor protein-tyrosine kinase erbB-25.95.95.9pIC504
Homo sapiensReceptor protein-tyrosine kinase erbB-26.36.37.1pKd2
Homo sapiensRibosomal protein S6 kinase alpha 25.15.15.1pKd4
Homo sapiensSerine/threonine-protein kinase 106.55.47pKd3
Homo sapiensSerine/threonine-protein kinase 17A6.76.77.2pKd2
Homo sapiensSerine/threonine-protein kinase 17B5.45.45.9pKd2
Homo sapiensSerine/threonine-protein kinase 26.46.46.6pKd2
Homo sapiensSerine/threonine-protein kinase 245.75.75.7pKd1
Homo sapiensSerine/threonine-protein kinase 255.55.55.5pKd1
Homo sapiensSerine/threonine-protein kinase 32B5.25.25.2pKd1
Homo sapiensSerine/threonine-protein kinase 335.45.45.4pKd1
Homo sapiensSerine/threonine-protein kinase 365.45.45.9pKd2
Homo sapiensSerine/threonine-protein kinase 38-like5.55.55.5pKd1
Homo sapiensSerine/threonine-protein kinase Chk15.75.75.7pKd1
Homo sapiensSerine/threonine-protein kinase DCLK35.35.35.3pKd1
Homo sapiensSerine/threonine-protein kinase GAK8.26.98.8pKd4
Homo sapiensSerine/threonine-protein kinase MARK15.45.45.4pKd1
Homo sapiensSerine/threonine-protein kinase MST15.45.45.4pKd2
Homo sapiensSerine/threonine-protein kinase MST25.65.65.6pKd1
Mus musculusSerine/threonine-protein kinase MST2666pKd1
Homo sapiensSerine/threonine-protein kinase Nek15.45.45.4pKd1
Homo sapiensSerine/threonine-protein kinase NEK26.26.26.2pIC501
Homo sapiensSerine/threonine-protein kinase NEK26.26.26.9pKd2
Homo sapiensSerine/threonine-protein kinase PAK 15.55.55.7pKd2
Homo sapiensSerine/threonine-protein kinase PCTAIRE-1555pKd1
Homo sapiensSerine/threonine-protein kinase SIK25.45.45.4pKd1
Homo sapiensSerine/threonine-protein kinase TNNI3K5.15.15.1pKd1
Homo sapiensSerine/threonine-protein kinase WEE16.166.8pKd3
Homo sapiensTRAF2- and NCK-interacting kinase6.85.97.4pKd3
Homo sapiensTyrosine- and threonine-specific cdc2-inhibitory kinase65.56pKd3
Homo sapiensTyrosine kinase non-receptor protein 25.35.36.1pKd2
Homo sapiensTyrosine-protein kinase ABL6.65.87pKd14
Homo sapiensTyrosine-protein kinase ABL26.46.46.8pKd2
Homo sapiensTyrosine-protein kinase BLK7.17.17.1pKd1
Homo sapiensTyrosine-protein kinase BMX5.15.15.1pKd1
Homo sapiensTyrosine-protein kinase BTK5.85.36.3pKd3
Homo sapiensTyrosine-protein kinase CSK5.55.55.6pKd2
Homo sapiensTyrosine-protein kinase FER5.15.16.6pKd2
Homo sapiensTyrosine-protein kinase FES5.25.25.2pKd1
Homo sapiensTyrosine-protein kinase FGR666pKd1
Homo sapiensTyrosine-protein kinase FRK6.76.26.7pKd3
Homo sapiensTyrosine-protein kinase FYN5.65.65.8pKd2
Homo sapiensTyrosine-protein kinase HCK5.65.65.9pKd3
Homo sapiensTyrosine-protein kinase ITK/TSK5.65.65.6pKd1
Homo sapiensTyrosine-protein kinase JAK25.75.75.7pKd2
Homo sapiensTyrosine-protein kinase JAK37.67.67.6pKd2
Homo sapiensTyrosine-protein kinase LCK777.4pKd2
Homo sapiensTyrosine-protein kinase Lyn666.1pKd2
Homo sapiensTyrosine-protein kinase receptor FLT35.65.55.7pKd3
Homo sapiensTyrosine-protein kinase receptor Tie-1666pKd1
Homo sapiensTyrosine-protein kinase receptor TYRO35.45.45.4pKd1
Homo sapiensTyrosine-protein kinase receptor UFO666pKd1
Homo sapiensTyrosine-protein kinase SRC6.66.66.9pKd2
Homo sapiensTyrosine-protein kinase SYK5.15.15.9pKd2
Homo sapiensTyrosine-protein kinase TIE-25.55.55.5pKd1
Homo sapiensTyrosine-protein kinase TXK5.35.35.3pKd1
Homo sapiensTyrosine-protein kinase YES666.1pKd2
Mus musculusULK3 kinase5.45.45.4pKd1
Homo sapiensUncharacterized aarF domain-containing protein kinase 45.25.25.2pKd1
Homo sapiensVascular endothelial growth factor receptor 25.55.55.5pIC501
Homo sapiensWee1-like protein kinase 26.36.36.3pKd1
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