5O2B - chain A (model B) | WNK lysine deficient protein kinase 3
Structure information
PDB:5O2B
PubMed:-
Release date:2017-06-28
Resolution:2.04 Å
 
Kinase:WNK3 (Wnk3)
Family:WNK
Group:Other
Species:HUMAN
 
Quality Score:8
Missing Residues:0
Missing Atoms:25
DFG conformation:in
αC-helix conformation:out
Salt bridge KIII.17 and EαC.24:No
 
 
ASP rotation (xDFG.81) :308°
PHE rotation (xDFG.82) :359°
Activation loop position:-3.4Å
αC-helix position:21Å
 
G-rich loop angle:55.2°
G-rich loop distance:15.7Å
G-rich loop rotation:32.6°
Other models from this PDB:
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond protein
I3
H-bond protein
I7
H-bond ligand
H-bond protein
Binding pocket sequence
UniprotIELGRGAFKTVYKVAWCELRFKEEAEMLKGLQPNIVRFYDSVLVTELMTSGTLKTYLKRHTRTPPIIHRDLKCDNIFIIGDLGLA
Structure:IELGRGAFKTVYKVAWCELRFKEEAEMLKGLQPNIVRFYDSVLVTELMTSGTLKTYLKRHTRTPPIIHRDLKCDNIFIIGDLGLA


Modified residues
No modified residues identified.
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 #
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  • COLORS
  • Interaction types
  • KLIFS (all res.)
  • KLIFS (interacting res.)
  • None
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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 I
151
2 E
152
3 L
153
4 G
154
5 R
155
6 G
156
7 A
157
8 F
158
9 K
159
10 T
160
11 V
161
12 Y
162
13 K
163
14 V
173
15 A
174
16 W
175
17 C
176
18 E
177
19 L
178
20 R
190
αC b.l IV
21 F
191
22 K
192
23 E
193
24 E
194
25 A
195
26 E
196
27 M
197
28 L
198
29 K
199
30 G
200
31 L
201
32 Q
202
33 P
204
34 N
205
35 I
206
36 V
207
37 R
208
38 F
209
39 Y
210
40 D
211
IV V GK hinge linker αD αE
41 S
212
42 V
224
43 L
225
44 V
226
45 T
227
46 E
228
47 L
229
48 M
230
49 T
231
50 S
232
51 G
233
52 T
234
53 L
235
54 K
236
55 T
237
56 Y
238
57 L
239
58 K
240
59 R
241
60 H
265
αE VI c.l VII VIII x
61 T
266
62 R
267
63 T
268
64 P
269
65 P
270
66 I
271
67 I
272
68 H
273
69 R
274
70 D
275
71 L
276
72 K
277
73 C
278
74 D
279
75 N
280
76 I
281
77 F
282
78 I
283
79 I
292
80 G
293
DFG a.l
81 D
294
82 L
295
83 G
296
84 L
297
85 A
298

Interaction pattern search
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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