6E6E - chain G (model C) | SRC proto-oncogene, non-receptor tyrosine kinase
Structure information
PDB:6E6E
PubMed:32509799
Release date:2019-07-31
Resolution:2.15 Å
 
Kinase:SRC
Family:Src
Group:TK
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 (4.2Å)
 
 
ASP rotation (xDFG.81) :342°
PHE rotation (xDFG.82) :10°
Activation loop position:-3.4Å
αC-helix position:16.9Å
 
G-rich loop angle:53.5°
G-rich loop distance:15.9Å
G-rich loop rotation:52.6°
Other models from this PDB:
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I11
H-bond ligand
H-bond protein
Binding pocket sequence
UniprotVKLGQGCFGEVWMVAIKTLAFLQEAQVMKKLREKLVQLYAVYIVTEYMSKGSLLDFLKGYVERMNYVHRDLRAANILVVADFGLA
Structure:VKLGQGCFGEVWMVAIKTLAFLQEAQVMKKLREKLVQLYAVYIVTEYMSKGSLLDFLKGYVERMNYVHRDLRAANILVVADFGLA


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: HVY
Ligand Name: N-(2-chloro-6-methylphenyl)-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-4-{[2-(propanoylamino)phenyl]amino}pyrimidine-5-carboxamide

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  • LABELS
  • KLIFS residue #
  • Amino Acid
  • None
  • 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 V
271
2 K
272
3 L
273
4 G
274
5 Q
275
6 G
276
7 C
277
8 F
278
9 G
279
10 E
280
11 V
281
12 W
282
13 M
283
14 V
292
15 A
293
16 I
294
17 K
295
18 T
296
19 L
297
20 A
306
αC b.l IV
21 F
307
22 L
308
23 Q
309
24 E
310
25 A
311
26 Q
312
27 V
313
28 M
314
29 K
315
30 K
316
31 L
317
32 R
318
33 E
320
34 K
321
35 L
322
36 V
323
37 Q
324
38 L
325
39 Y
326
40 A
327
IV V GK hinge linker αD αE
41 V
328
42 Y
335
43 I
336
44 V
337
45 T
338
46 E
339
47 Y
340
48 M
341
49 S
342
50 K
343
51 G
344
52 S
345
53 L
346
54 L
347
55 D
348
56 F
349
57 L
350
58 K
351
59 G
352
60 Y
376
αE VI c.l VII VIII x
61 V
377
62 E
378
63 R
379
64 M
380
65 N
381
66 Y
382
67 V
383
68 H
384
69 R
385
70 D
386
71 L
387
72 R
388
73 A
389
74 A
390
75 N
391
76 I
392
77 L
393
78 V
394
79 V
402
80 A
403
DFG a.l
81 D
404
82 F
405
83 G
406
84 L
407
85 A
408

Interaction pattern search
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Binding affinities
ChEMBL ID:CHEMBL4548584
Bioaffinities: 1 record for 1 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensTyrosine-protein kinase SRC8.58.58.5pIC501