5WDY - chain B (model B) | WNK lysine deficient protein kinase 1
Structure information
PDB:5WDY
PubMed:28771350
Release date:2017-08-16
Resolution:2.46 Å
 
Kinase:WNK1 (Wnk1)
Family:WNK
Group:Other
Species:HUMAN
 
Quality Score:8
Missing Residues:0
Missing Atoms:0
DFG conformation:in
αC-helix conformation:out
Salt bridge KIII.17 and EαC.24:No
 
 
ASP rotation (xDFG.81) :343°
PHE rotation (xDFG.82) :357°
Activation loop position:-3.3Å
αC-helix position:22Å
 
G-rich loop angle:60°
G-rich loop distance:16.8Å
G-rich loop rotation:34.4°
Other models from this PDB:
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
No waters were found in the defined clusters
Binding pocket sequence
UniprotIEIGRGSFKTVYKVAWCELRFKEEAEMLKGLQPNIVRFYDSVLVTELMTSGTLKTYLKRHTRTPPIIHRDLKCDNIFIIGDLGLA
Structure:IEIGRGSFKTVYKVAWCELRFKEEAEMLKGLQPNIVRFYDSVLVTELMTSGTLKTYLKRHTRTPPIIHRDLKCDNIFIIGDLGLA


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: ANP
Ligand Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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  • LABELS
  • KLIFS residue #
  • Amino Acid
  • None
  • COLORS
  • Interaction types
  • KLIFS (all res.)
  • KLIFS (interacting res.)
  • None
  • 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 I
225
2 E
226
3 I
227
4 G
228
5 R
229
6 G
230
7 S
231
8 F
232
9 K
233
10 T
234
11 V
235
12 Y
236
13 K
237
14 V
247
15 A
248
16 W
249
17 C
250
18 E
251
19 L
252
20 R
264
αC b.l IV
21 F
265
22 K
266
23 E
267
24 E
268
25 A
269
26 E
270
27 M
271
28 L
272
29 K
273
30 G
274
31 L
275
32 Q
276
33 P
278
34 N
279
35 I
280
36 V
281
37 R
282
38 F
283
39 Y
284
40 D
285
IV V GK hinge linker αD αE
41 S
286
42 V
298
43 L
299
44 V
300
45 T
301
46 E
302
47 L
303
48 M
304
49 T
305
50 S
306
51 G
307
52 T
308
53 L
309
54 K
310
55 T
311
56 Y
312
57 L
313
58 K
314
59 R
315
60 H
339
αE VI c.l VII VIII x
61 T
340
62 R
341
63 T
342
64 P
343
65 P
344
66 I
345
67 I
346
68 H
347
69 R
348
70 D
349
71 L
350
72 K
351
73 C
352
74 D
353
75 N
354
76 I
355
77 F
356
78 I
357
79 I
366
80 G
367
DFG a.l
81 D
368
82 L
369
83 G
370
84 L
371
85 A
372

Interaction pattern search
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Binding affinities
ChEMBL ID:CHEMBL1230989

Bioaffinities: No (p)Ki/(p)IC50/(p)EC50 values for kinases found (with a ChEMBL confidence ≥ 8).