4QMM - chain A | Serine/threonine kinase 24
Structure information
PDB:4QMM
PubMed:27135311
Release date:2015-07-01
Resolution:1.85 Å
 
Kinase:STK24 (MST3)
Family:STE20
Group:STE
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) :352°
PHE rotation (xDFG.82) :12°
Activation loop position:-3.3Å
αC-helix position:17.8Å
 
G-rich loop angle:54.2°
G-rich loop distance:15.7Å
G-rich loop rotation:76°
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I2
H-bond protein
I3
H-bond protein
I4
H-bond protein
I5
H-bond protein
I10
H-bond ligand
H-bond protein
Binding pocket sequence
UniprotEKIGKGSFGEVFKVAIKIIDIQQEITVLSQCDPYVTKYYGSWIIMEYLGGGSALDLLEPYLHSEKKIHRDIKAANVLLLADFGVA
Structure:EKIGKGSFGEVFKVAIKIIDIQQEITVLSQCDPYVTKYYGSWIIMEYLGGGSALDLLEPYLHSEKKIHRDIKAANVLLLADFGVA


Modified residues
Residue 178 (not in pocket)
Phosphorylated threonine
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: 35R
Ligand Name: 1-cyclopropyl-3-{3-[5-(morpholin-4-ylmethyl)-1H-benzimidazol-2-yl]-1H-pyrazol-4-yl}urea

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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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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 E
28
2 K
29
3 I
30
4 G
31
5 K
32
6 G
33
7 S
34
8 F
35
9 G
36
10 E
37
11 V
38
12 F
39
13 K
40
14 V
50
15 A
51
16 I
52
17 K
53
18 I
54
19 I
55
20 D
66
αC b.l IV
21 I
67
22 Q
68
23 Q
69
24 E
70
25 I
71
26 T
72
27 V
73
28 L
74
29 S
75
30 Q
76
31 C
77
32 D
78
33 P
80
34 Y
81
35 V
82
36 T
83
37 K
84
38 Y
85
39 Y
86
40 G
87
IV V GK hinge linker αD αE
41 S
88
42 W
96
43 I
97
44 I
98
45 M
99
46 E
100
47 Y
101
48 L
102
49 G
103
50 G
104
51 G
105
52 S
106
53 A
107
54 L
108
55 D
109
56 L
110
57 L
111
58 E
112
59 P
113
60 Y
134
αE VI c.l VII VIII x
61 L
135
62 H
136
63 S
137
64 E
138
65 K
139
66 K
140
67 I
141
68 H
142
69 R
143
70 D
144
71 I
145
72 K
146
73 A
147
74 A
148
75 N
149
76 V
150
77 L
151
78 L
152
79 L
160
80 A
161
DFG a.l
81 D
162
82 F
163
83 G
164
84 V
165
85 A
166

Interaction pattern search
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Binding affinities
ChEMBL ID:CHEMBL495727
Bioaffinities: 166 records for 123 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensActivin receptor type-17.17.17.1pKd1
Homo sapiensActivin receptor type-1B6.16.16.1pKd1
Homo sapiensAdaptor-associated kinase7.87.87.8pKd1
Homo sapiensAMP-activated protein kinase, alpha-1 subunit7.37.37.3pKd1
Homo sapiensAMP-activated protein kinase, gamma-1 subunit7.57.57.5pKd1
Homo sapiensAMP-activated protein kinase, gamma-2 subunit7.27.27.2pKd1
Homo sapiensBMP-2-inducible protein kinase7.57.57.5pKd1
Homo sapiensBone morphogenetic protein receptor type-1A6.46.46.4pKd1
Homo sapiensBone morphogenetic protein receptor type-1B7.77.77.7pKd1
Homo sapiensBone morphogenetic protein receptor type-27.47.47.4pKd1
Homo sapiensBreakpoint cluster region protein6.86.86.8pKd2
Homo sapienscAMP-dependent protein kinase alpha-catalytic subunit5.55.55.5pKd1
Homo sapienscAMP-dependent protein kinase beta-1 catalytic subunit666pKd1
Homo sapienscAMP-dependent protein kinase, gamma catalytic subunit8.58.58.5pKd1
Homo sapiensCasein kinase II alpha (prime)7.27.27.2pKd1
Homo sapiensCell division cycle 7-related protein kinase6.36.36.3pKd1
Homo sapiensc-Jun N-terminal kinase 16.86.86.8pKd1
Homo sapiensc-Jun N-terminal kinase 26.36.36.3pKd1
Homo sapiensc-Jun N-terminal kinase 36.56.56.5pKd1
Homo sapiensCyclin-dependent kinase 108.18.18.1pKd1
Homo sapiensCyclin-dependent kinase 45.95.95.9pKd1
Homo sapiensCyclin-dependent kinase 55.95.95.9pKd1
Homo sapiensCyclin-dependent kinase 66.96.96.9pKd1
Homo sapiensCyclin-dependent kinase 95.85.85.8pKd1
Homo sapiensDual specificity mitogen-activated protein kinase kinase 57.37.37.3pKd1
Homo sapiensDual specificity mitogen-activated protein kinase kinase 65.55.55.5pKd1
Homo sapiensDual-specificity tyrosine-phosphorylation regulated kinase 1A5.65.65.6pKd1
Homo sapiensDual specificty protein kinase CLK15.75.75.7pKd1
Homo sapiensEphrin type-A receptor 25.85.85.8pKd1
Homo sapiensEphrin type-A receptor 44.44.44.4pKd1
Homo sapiensEphrin type-A receptor 78.18.18.1pKd1
Homo sapiensEphrin type-B receptor 67.97.97.9pKd1
Homo sapiensFibroblast growth factor receptor 1888pIC502
Homo sapiensFibroblast growth factor receptor 17.67.67.6pKd1
Homo sapiensFibroblast growth factor receptor 2889pIC502
Homo sapiensFibroblast growth factor receptor 3888pIC501
Homo sapiensGlycogen synthase kinase-3 alpha8.28.28.2pKd1
Homo sapiensGlycogen synthase kinase-3 beta999pIC501
Homo sapiensGlycogen synthase kinase-3 beta8.28.28.2pKd1
Homo sapiensG protein-coupled receptor kinase 64.94.94.9pKd1
Homo sapiensHepatocyte growth factor receptor8.28.28.2pKd1
Homo sapiensInhibitor of nuclear factor kappa B kinase epsilon subunit6.76.76.7pKd1
Homo sapiensLIM domain kinase 15.85.85.8pKd1
Homo sapiensLIM domain kinase 25.45.45.4pKd1
Homo sapiensMAP kinase-activated protein kinase 56.26.26.2pKd1
Homo sapiensMAP/microtubule affinity-regulating kinase 25.95.95.9pKd1
Homo sapiensMaternal embryonic leucine zipper kinase6.26.26.2pIC501
Homo sapiensMaternal embryonic leucine zipper kinase5.85.85.8pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase 15.95.95.9pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase 117.37.37.3pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase 26.66.66.6pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase 36.56.56.5pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase 54.64.64.6pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 16.76.76.7pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 4777pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 55.75.75.7pKd1
Homo sapiensMitotic checkpoint serine/threonine-protein kinase BUB1777pKd1
Homo sapiensMyosin light chain kinase6.96.96.9pKd1
Homo sapiensPlatelet-derived growth factor receptor alpha888pIC501
Homo sapiensProtein kinase C alpha5.85.85.8pKd1
Homo sapiensProtein kinase C beta5.55.55.5pKd1
Homo sapiensProtein kinase C mu888pIC501
Homo sapiensProtein kinase C nu6.36.36.3pKd1
Homo sapiensProtein kinase N15.55.55.5pKd1
Homo sapiensProtein kinase N25.65.65.6pKd1
Homo sapiensProto-oncogene tyrosine-protein kinase MER999pIC501
Homo sapiensPyruvate dehydrogenase kinase isoform 1888pIC501
Homo sapiensRibosomal protein S6 kinase 16.96.96.9pKd1
Homo sapiensRibosomal protein S6 kinase alpha 16.36.36.3pKd2
Homo sapiensRibosomal protein S6 kinase alpha 2999pIC502
Homo sapiensRibosomal protein S6 kinase alpha 3999pIC502
Homo sapiensRibosomal protein S6 kinase alpha 3777pKd2
Homo sapiensRibosomal protein S6 kinase alpha 4888pIC502
Homo sapiensRibosomal protein S6 kinase alpha 47.17.17.1pKd2
Homo sapiensRibosomal protein S6 kinase alpha 55.95.95.9pKd2
Homo sapiensRibosomal protein S6 kinase alpha 67.87.87.8pKd2
Homo sapiensSerine/threonine-protein kinase 107.17.17.1pKd1
Homo sapiensSerine/threonine-protein kinase 165.95.95.9pKd1
Homo sapiensSerine/threonine-protein kinase 17A888pIC501
Homo sapiensSerine/threonine-protein kinase 26.46.46.4pKd1
Homo sapiensSerine/threonine-protein kinase Aurora-A8.58.58.5pIC502
Homo sapiensSerine/threonine-protein kinase Aurora-A7.37.37.8pKd2
Homo sapiensSerine/threonine-protein kinase Aurora-B7.57.58.6pIC504
Homo sapiensSerine/threonine-protein kinase Aurora-B7.87.87.8pKd1
Homo sapiensSerine/threonine-protein kinase Chk17.17.17.1pKd1
Homo sapiensSerine/threonine-protein kinase c-TAK15.95.95.9pKd1
Homo sapiensSerine/threonine-protein kinase D26.66.66.6pKd1
Homo sapiensSerine/threonine-protein kinase GAK5.85.85.8pKd1
Homo sapiensSerine/threonine-protein kinase LATS17.47.47.4pKd1
Homo sapiensSerine/threonine-protein kinase Nek35.75.75.7pKd1
Homo sapiensSerine/threonine-protein kinase NEK95.85.85.8pKd1
Homo sapiensSerine/threonine-protein kinase PAK 4777pKd1
Homo sapiensSerine/threonine-protein kinase PAK66.76.76.7pKd1
Homo sapiensSerine/threonine-protein kinase PCTAIRE-17.57.57.5pKd1
Homo sapiensSerine/threonine-protein kinase PCTAIRE-25.95.95.9pKd1
Homo sapiensSerine/threonine-protein kinase PLK47.77.77.7pKd1
Homo sapiensSerine/threonine-protein kinase receptor R37.87.87.8pKd1
Homo sapiensSerine/threonine-protein kinase SIK27.57.57.5pKd1
Homo sapiensSerine/threonine-protein kinase SIK35.45.45.4pKd1
Homo sapiensSerine/threonine-protein kinase TAO15.75.75.7pKd1
Homo sapiensSerine/threonine-protein kinase TBK1777pKd1
Homo sapiensSerine/threonine-protein kinase ULK37.47.47.4pKd1
Homo sapiensTGF-beta receptor type I7.17.17.1pKd1
Homo sapiensTGF-beta receptor type II5.95.95.9pKd1
Homo sapiensTRAF2- and NCK-interacting kinase6.16.16.1pKd1
Homo sapiensTyrosine-protein kinase ABL8.488.4pIC503
Homo sapiensTyrosine-protein kinase ABL6.56.56.5pKd1
Homo sapiensTyrosine-protein kinase ABL2666pKd1
Homo sapiensTyrosine-protein kinase BRK6.76.76.7pKd1
Homo sapiensTyrosine-protein kinase BTK6.36.36.3pKd1
Homo sapiensTyrosine-protein kinase CSK5.85.85.8pKd1
Homo sapiensTyrosine-protein kinase FER6.56.56.5pKd1
Homo sapiensTyrosine-protein kinase FGR5.85.85.8pKd1
Homo sapiensTyrosine-protein kinase FYN6.36.36.3pKd1
Homo sapiensTyrosine-protein kinase HCK6.26.26.2pKd1
Homo sapiensTyrosine-protein kinase JAK16.46.46.4pKd2
Homo sapiensTyrosine-protein kinase JAK28.98.99pIC504
Homo sapiensTyrosine-protein kinase JAK2888pKd2
Homo sapiensTyrosine-protein kinase JAK3999pIC504
Homo sapiensTyrosine-protein kinase LCK6.16.16.1pKd1
Homo sapiensTyrosine-protein kinase Lyn5.95.95.9pKd1
Homo sapiensTyrosine-protein kinase receptor FLT3888pIC502
Homo sapiensTyrosine-protein kinase receptor FLT37.27.27.2pKd1
Homo sapiensTyrosine-protein kinase receptor RET999pIC501
Homo sapiensTyrosine-protein kinase receptor RET888pKd1
Homo sapiensTyrosine-protein kinase SRC888pIC501
Homo sapiensTyrosine-protein kinase SRC6.26.26.2pKd1
Homo sapiensTyrosine-protein kinase SYK6.96.96.9pKd1
Homo sapiensTyrosine-protein kinase TEC6.96.96.9pKd1
Homo sapiensTyrosine-protein kinase TYK2999pIC502
Homo sapiensTyrosine-protein kinase TYK26.66.66.6pKd2
Homo sapiensTyrosine-protein kinase YES999pIC501
Homo sapiensTyrosine-protein kinase YES6.26.26.2pKd1
Homo sapiensUncharacterized aarF domain-containing protein kinase 16.36.36.3pKd1
Homo sapiensVascular endothelial growth factor receptor 1888pIC501
Homo sapiensVascular endothelial growth factor receptor 2888pIC501
Homo sapiensVascular endothelial growth factor receptor 3999pIC501