3MY0 - chain N | Activin A receptor type IL
Structure information
PDB:3MY0
PubMed:25557927
Release date:2010-07-21
Resolution:2.65 Å
 
Kinase:ACVRL1 (ALK1)
Family:STKR
Group:TKL
Species:HUMAN
 
Quality Score:8.2
Missing Residues:0
Missing Atoms:18
DFG conformation:in
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:No (4.6Å)
 
 
ASP rotation (xDFG.81) :346°
PHE rotation (xDFG.82) :
Activation loop position:-3.4Å
αC-helix position:17.2Å
 
G-rich loop angle:53.8°
G-rich loop distance:16.6Å
G-rich loop rotation:43.5°
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
UniprotECVGKGRYGEVWRVAVKIFSWFRETEIYNTVLDNILGFIASWLITHYHEHGSLYDFLQRTQGKPAIAHRDFKSRNVLVIADLGLA
Structure:ECVGKGRYGEVWRVAVKIFSWFRETEIYNTVLDNILGFIASWLITHYHEHGSLYDFLQRTQGKPAIAHRDFKSRNVLVIADLGLA


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: LDN
Ligand Name: 4-[6-(4-piperazin-1-ylphenyl)pyrazolo[1,5-a]pyrimidin-3-yl]quinoline

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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 E
206
2 C
207
3 V
208
4 G
209
5 K
210
6 G
211
7 R
212
8 Y
213
9 G
214
10 E
215
11 V
216
12 W
217
13 R
218
14 V
226
15 A
227
16 V
228
17 K
229
18 I
230
19 F
231
20 S
238
αC b.l IV
21 W
239
22 F
240
23 R
241
24 E
242
25 T
243
26 E
244
27 I
245
28 Y
246
29 N
247
30 T
248
31 V
249
32 L
250
33 D
254
34 N
255
35 I
256
36 L
257
37 G
258
38 F
259
39 I
260
40 A
261
IV V GK hinge linker αD αE
41 S
262
42 W
274
43 L
275
44 I
276
45 T
277
46 H
278
47 Y
279
48 H
280
49 E
281
50 H
282
51 G
283
52 S
284
53 L
285
54 Y
286
55 D
287
56 F
288
57 L
289
58 Q
290
59 R
291
60 T
320
αE VI c.l VII VIII x
61 Q
321
62 G
322
63 K
323
64 P
324
65 A
325
66 I
326
67 A
327
68 H
328
69 R
329
70 D
330
71 F
331
72 K
332
73 S
333
74 R
334
75 N
335
76 V
336
77 L
337
78 V
338
79 I
346
80 A
347
DFG a.l
81 D
348
82 L
349
83 G
350
84 L
351
85 A
352

Interaction pattern search
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Binding affinities
ChEMBL ID:CHEMBL513147
Bioaffinities: 30 records for 11 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensActivin receptor type-17.87.48.5pIC506
Mus musculusActivin receptor type-17.97.97.9pEC501
Homo sapiensActivin receptor type-1B6.55.77.4pIC503
Homo sapiensAMP-activated protein kinase, beta-1 subunit666pIC501
Homo sapiensBone morphogenetic protein receptor type-1A7.77.68.7pIC503
Homo sapiensBone morphogenetic protein receptor type-1B7.97.29pIC503
Homo sapiensBone morphogenetic protein receptor type-25.45.45.4pIC501
Homo sapiensSerine/threonine-protein kinase receptor R37.97.78pIC503
Homo sapiensTGF-beta receptor type I6.36.37.6pIC506
Homo sapiensTGF-beta receptor type II6.86.86.9pIC502
Homo sapiensVascular endothelial growth factor receptor 26.76.76.7pIC501