2H8H - chain A (model B) | SRC proto-oncogene, non-receptor tyrosine kinase
Structure information
PDB:2H8H
PubMed:17064066
Release date:2006-11-21
Resolution:2.2 Å
 
Kinase:SRC
Family:Src
Group:TK
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 (13.6Å)
 
 
ASP rotation (xDFG.81) :334°
PHE rotation (xDFG.82) :329°
Activation loop position:-4.5Å
αC-helix position:21.2Å
 
G-rich loop angle:53.4°
G-rich loop distance:16.3Å
G-rich loop rotation:46.1°
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
I5
H-bond protein
I6
H-bond ligand
H-bond protein
Binding pocket sequence
UniprotVKLGQGCFGEVWMVAIKTLAFLQEAQVMKKLREKLVQLYAVYIVTEYMSKGSLLDFLKGYVERMNYVHRDLRAANILVVADFGLA
Structure:VKLGQGCFGEVWMVAIKTLAFLQEAQVMKKLREKLVQLYAVYIVTEYMSKGSLLDFLKGYVERMNYVHRDLRAANILVVADFGLA


Modified residues
Residue 527 (not in pocket)
Phosphorylated tyrosine
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: H8H
Ligand Name: N-(5-CHLORO-1,3-BENZODIOXOL-4-YL)-7-[2-(4-METHYLPIPERAZIN-1-YL)ETHOXY]-5-(TETRAHYDRO-2H-PYRAN-4-YLOXY)QUINAZOLIN-4-AMINE

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  • LABELS
  • KLIFS residue #
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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 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:CHEMBL217092
Bioaffinities: 83 records for 51 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensActivin receptor type-18.48.48.4pKd1
Homo sapiensActivin receptor type-1B6.96.96.9pKd1
Homo sapiensActivin receptor type-2B5.45.45.4pKd1
Homo sapiensBone morphogenetic protein receptor type-1A7.27.27.2pKd1
Homo sapiensBone morphogenetic protein receptor type-1B7.57.57.5pKd1
Homo sapiensBreakpoint cluster region protein7.87.87.8pKd2
Homo sapiensChaperone activity of bc1 complex-like, mitochondrial6.66.66.6pKd1
Homo sapiensCyclin-dependent kinase 2555pIC501
Homo sapiensDiscoidin domain-containing receptor 24.44.44.4pKd1
Homo sapiensEphrin type-A receptor 1888pKd1
Homo sapiensEphrin type-A receptor 26.16.16.1pKd1
Homo sapiensEphrin type-A receptor 4666pKd1
Homo sapiensEphrin type-A receptor 55.65.65.6pKd1
Homo sapiensEphrin type-B receptor 2555pKd1
Homo sapiensEphrin type-B receptor 45.45.45.4pKd1
Homo sapiensEphrin type-B receptor 65.45.45.4pKd1
Homo sapiensEpidermal growth factor receptor erbB15.65.67.2pIC504
Homo sapiensEpithelial discoidin domain-containing receptor 15.45.45.4pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 4666pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 54.64.64.6pKd1
Homo sapiensMixed lineage kinase 75.55.55.5pKd1
Homo sapiensPlatelet-derived growth factor receptor alpha555pIC501
Homo sapiensPlatelet-derived growth factor receptor beta6.26.26.2pKd1
Homo sapiensReceptor-interacting serine/threonine-protein kinase 35.85.85.8pKd1
Homo sapiensSerine/threonine-protein kinase 104.94.94.9pKd1
Homo sapiensSerine/threonine-protein kinase 24.54.54.5pKd1
Homo sapiensSerine/threonine-protein kinase GAK777pKd1
Homo sapiensSerine/threonine-protein kinase RIPK28.78.78.7pKd1
Homo sapiensSerine/threonine-protein kinase SIK25.95.95.9pKd1
Homo sapiensSerine/threonine-protein kinase SIK35.35.35.3pKd1
Homo sapiensStem cell growth factor receptor6.76.76.7pIC503
Homo sapiensTGF-beta receptor type I6.76.76.7pKd1
Homo sapiensTRAF2- and NCK-interacting kinase5.95.95.9pKd1
Homo sapiensTyrosine- and threonine-specific cdc2-inhibitory kinase556.4pIC502
Homo sapiensTyrosine- and threonine-specific cdc2-inhibitory kinase5.65.65.6pKd1
Homo sapiensTyrosine- and threonine-specific cdc2-inhibitory kinase5.35.37.4pKi2
Homo sapiensTyrosine kinase non-receptor protein 25.35.35.3pKd1
Homo sapiensTyrosine-protein kinase ABL7.57.57.5pIC503
Homo sapiensTyrosine-protein kinase ABL7.37.37.3pKd1
Homo sapiensTyrosine-protein kinase ABL2777pKd1
Homo sapiensTyrosine-protein kinase BRK6.36.36.3pKd1
Homo sapiensTyrosine-protein kinase BTK555pKd1
Homo sapiensTyrosine-protein kinase CSK6.16.16.1pIC503
Homo sapiensTyrosine-protein kinase CSK4.44.44.4pKd1
Homo sapiensTyrosine-protein kinase FGR666pKd1
Homo sapiensTyrosine-protein kinase FRK5.65.65.6pKd1
Homo sapiensTyrosine-protein kinase FYN777pKd1
Homo sapiensTyrosine-protein kinase HCK777pKd1
Homo sapiensTyrosine-protein kinase LCK8.48.48.4pIC501
Homo sapiensTyrosine-protein kinase LCK8.18.18.1pKd1
Homo sapiensTyrosine-protein kinase Lyn777pKd1
Homo sapiensTyrosine-protein kinase receptor FLT36.96.96.9pKd1
Homo sapiensTyrosine-protein kinase receptor RET6.86.86.8pKd1
Homo sapiensTyrosine-protein kinase SRC8.67.19pIC509
Homo sapiensTyrosine-protein kinase SRC6.96.96.9pKd1
Homo sapiensTyrosine-protein kinase YES8.48.29.2pIC505
Homo sapiensTyrosine-protein kinase YES777pKd1
Homo sapiensVascular endothelial growth factor receptor 24.74.74.7pIC502