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  4QMW - chain A (model B) | Serine/threonine kinase 24
Structure information
PDB:4QMW
PubMed:27135311
Release date:2015-07-01
Resolution:1.6 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 (2.4Å)
 
 
ASP rotation (xDFG.81) :341°
PHE rotation (xDFG.82) :15°
Activation loop position:-3.2Å
αC-helix position:17.2Å
 
G-rich loop angle:59.2°
G-rich loop distance:17.2Å
G-rich loop rotation:67.4°
Other models from this PDB:
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I1
No H-bonds
I2
H-bond protein
I3
No H-bonds
I7
H-bond ligand
I10
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: KS1
Ligand Name: 1-cyclopentyl-3-(1H-pyrrolo[2,3-b]pyridin-5-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine

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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
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:CHEMBL1081312
Bioaffinities: 76 records for 59 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensActivin receptor type-17.27.27.2pKi1
Homo sapiensALK tyrosine kinase receptor6.26.26.2pKi1
Homo sapiensAMP-activated protein kinase, alpha-1 subunit5.65.65.6pKi1
Homo sapienscAMP-dependent protein kinase alpha-catalytic subunit6.16.16.1pKi1
Homo sapiensCasein kinase I alpha7.47.47.4pKi1
Homo sapiensCell division protein kinase 85.95.95.9pKi1
Homo sapiensc-Jun N-terminal kinase 15.65.65.6pKi1
Homo sapiensc-Jun N-terminal kinase 25.95.95.9pKi1
Homo sapiensCyclin-dependent kinase 55.95.95.9pKi1
Homo sapiensDeath-associated protein kinase 35.35.35.3pKi1
Homo sapiensDNA-dependent protein kinase7.27.27.2pIC501
Homo sapiensDual specificity mitogen-activated protein kinase kinase 16.46.46.4pKi1
Homo sapiensDual specificity mitogen-activated protein kinase kinase 2666pKi1
Homo sapiensDual specificity protein kinase CLK2666pKi1
Homo sapiensDual specificity protein kinase CLK46.16.16.1pKi1
Homo sapiensEphrin type-B receptor 46.76.76.7pIC501
Homo sapiensEpidermal growth factor receptor erbB16.66.66.6pIC502
Homo sapiensFibroblast growth factor receptor 1777pKi1
Homo sapiensFocal adhesion kinase 15.95.95.9pKi1
Homo sapiensGlycogen synthase kinase-3 alpha5.75.75.7pKi1
Homo sapiensInhibitor of nuclear factor kappa B kinase epsilon subunit5.85.85.8pKi1
Homo sapiensInsulin-like growth factor I receptor6.46.46.4pKi1
Homo sapiensLeucine-rich repeat serine/threonine-protein kinase 27.27.27.2pKi1
Homo sapiensLeukocyte tyrosine kinase receptor6.86.86.8pKi1
Homo sapiensLIM domain kinase 16.86.86.8pKi1
Homo sapiensMacrophage colony stimulating factor receptor6.46.46.4pKi1
Homo sapiensMacrophage-stimulating protein receptor6.96.96.9pKi1
Homo sapiensMAP kinase p38 alpha5.65.65.6pKi1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 26.56.56.5pKi1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 46.26.26.2pKi1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 55.95.95.9pKi1
Homo sapiensPI3-kinase p110-alpha subunit7.37.37.3pIC503
Homo sapiensPI3-kinase p110-beta subunit5.95.95.9pIC502
Homo sapiensPI3-kinase p110-delta subunit6.86.86.8pIC502
Homo sapiensPI3-kinase p110-gamma subunit666pIC502
Homo sapiensPI4-kinase beta subunit7.27.27.2pIC501
Homo sapiensPlatelet-derived growth factor receptor alpha6.56.56.5pKi1
Homo sapiensPlatelet-derived growth factor receptor beta6.46.46.4pKi1
Homo sapiensProtein kinase C nu6.66.66.6pKi1
Homo sapiensProtein kinase C theta6.36.36.3pKi1
Homo sapiensRho-associated protein kinase 16.76.76.7pKi1
Homo sapiensRho-associated protein kinase 27.47.47.4pKi1
Homo sapiensSerine-protein kinase ATR5.95.95.9pIC501
Homo sapiensSerine/threonine-protein kinase c-TAK16.16.16.1pKi1
Homo sapiensSerine/threonine-protein kinase mTOR888pIC502
Homo sapiensSerine/threonine-protein kinase PAK 46.26.26.2pKi1
Homo sapiensSerine/threonine-protein kinase TAO15.65.65.6pKi1
Homo sapiensTyrosine kinase non-receptor protein 26.46.46.4pKi1
Homo sapiensTyrosine-protein kinase ABL7.87.88.7pIC503
Homo sapiensTyrosine-protein kinase ABL7.87.87.8pKi1
Homo sapiensTyrosine-protein kinase BTK5.85.85.8pKi1
Homo sapiensTyrosine-protein kinase FYN7.17.17.1pKi1
Homo sapiensTyrosine-protein kinase HCK8.18.18.1pIC502
Homo sapiensTyrosine-protein kinase JAK2666pKi2
Homo sapiensTyrosine-protein kinase LCK6.86.86.8pKi1
Homo sapiensTyrosine-protein kinase receptor RET8.98.98.9pKi1
Homo sapiensTyrosine-protein kinase receptor TYRO36.16.16.1pKi1
Homo sapiensTyrosine-protein kinase SRC7.97.97.9pIC503
Homo sapiensVascular endothelial growth factor receptor 17.27.27.2pKi1
Homo sapiensVascular endothelial growth factor receptor 27.97.47.9pIC503
Homo sapiensVascular endothelial growth factor receptor 28.38.38.3pKi1
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