5QIN - chain A (model B) | Transforming growth factor beta receptor II
Structure information
PDB:5QIN
PubMed:30429955
Release date:2018-10-31
Resolution:1.57 Å
 
Kinase:TGFBR2 (TGFbR2)
Family:STKR
Group:TKL
Species:HUMAN
 
Quality Score:9.4
Missing Residues:0
Missing Atoms:6
DFG conformation:in
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:Yes (3Å)
 
 
ASP rotation (xDFG.81) :349°
PHE rotation (xDFG.82) :22°
Activation loop position:-2.9Å
αC-helix position:17.1Å
 
G-rich loop angle:45.2°
G-rich loop distance:13.8Å
G-rich loop rotation:63.2°
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 ligand
H-bond protein
I5
H-bond ligand
H-bond protein
I9
H-bond ligand
H-bond protein
Binding pocket sequence
UniprotTLVGKGRFAEVYKVAVKIFSWKTEKDIFSDINENILQFLTAWLITAFHAKGNLQEYLTRGRPKMPIVHRDLKSSNILVLCDFGLS
Structure:TLVGKGRFAEVYKVAVKIFSWKTEKDIFSDINENILQFLTAWLITAFHAKGNLQEYLTRGRPKMPIVHRDLKSSNILVLCDFGLS


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: J2V
Ligand Name: N-{4-[3-(6-methoxypyridin-3-yl)-1H-pyrrolo[3,2-b]pyridin-2-yl]pyridin-2-yl}acetamide

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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 T
248
2 L
249
3 V
250
4 G
251
5 K
252
6 G
253
7 R
254
8 F
255
9 A
256
10 E
257
11 V
258
12 Y
259
13 K
260
14 V
274
15 A
275
16 V
276
17 K
277
18 I
278
19 F
279
20 S
286
αC b.l IV
21 W
287
22 K
288
23 T
289
24 E
290
25 K
291
26 D
292
27 I
293
28 F
294
29 S
295
30 D
296
31 I
297
32 N
298
33 E
302
34 N
303
35 I
304
36 L
305
37 Q
306
38 F
307
39 L
308
40 T
309
IV V GK hinge linker αD αE
41 A
310
42 W
322
43 L
323
44 I
324
45 T
325
46 A
326
47 F
327
48 H
328
49 A
329
50 K
330
51 G
331
52 N
332
53 L
333
54 Q
334
55 E
335
56 Y
336
57 L
337
58 T
338
59 R
339
60 G
369
αE VI c.l VII VIII x
61 R
370
62 P
371
63 K
372
64 M
373
65 P
374
66 I
375
67 V
376
68 H
377
69 R
378
70 D
379
71 L
380
72 K
381
73 S
382
74 S
383
75 N
384
76 I
385
77 L
386
78 V
387
79 L
395
80 C
396
DFG a.l
81 D
397
82 F
398
83 G
399
84 L
400
85 S
401

Interaction pattern search
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Binding affinities
ChEMBL ID:CHEMBL4279160
Bioaffinities: 2 records for 2 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensTGF-beta receptor type I8.58.58.5pIC501
Homo sapiensTGF-beta receptor type II7.47.47.4pIC501