3HMI - chain A (model A) | ABL proto-oncogene 2, non-receptor tyrosine kinase
Structure information
PDB:3HMI
PubMed:-
Release date:2009-07-07
Resolution:1.65 Å
 
Kinase:ABL2
Family:Abl
Group:TK
Species:HUMAN
 
Quality Score:9.5
Missing Residues:0
Missing Atoms:5
DFG conformation:out-like
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:Yes (2.5Å)
 
 
ASP rotation (xDFG.81) :110°
PHE rotation (xDFG.82) :247°
Activation loop position:-1.2Å
αC-helix position:19.2Å
 
G-rich loop angle:56.7°
G-rich loop distance:16.7Å
G-rich loop rotation:16.1°
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 ligand
H-bond protein
I5
H-bond protein
Binding pocket sequence
UniprotHKLGGGQYGEVYVVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIVTEYMPYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS
Structure:HKLGGGQYGEVYVVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIVTEYMPYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: DKI
Ligand Name: 5-AMINO-3-{[4-(AMINOSULFONYL)PHENYL]AMINO}-N-(2,6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE

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  • LABELS
  • KLIFS residue #
  • Amino Acid
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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 H
292
2 K
293
3 L
294
4 G
295
5 G
296
6 G
297
7 Q
298
8 Y
299
9 G
300
10 E
301
11 V
302
12 Y
303
13 V
304
14 V
314
15 A
315
16 V
316
17 K
317
18 T
318
19 L
319
20 E
328
αC b.l IV
21 F
329
22 L
330
23 K
331
24 E
332
25 A
333
26 A
334
27 V
335
28 M
336
29 K
337
30 E
338
31 I
339
32 K
340
33 P
342
34 N
343
35 L
344
36 V
345
37 Q
346
38 L
347
39 L
348
40 G
349
IV V GK hinge linker αD αE
41 V
350
42 Y
358
43 I
359
44 V
360
45 T
361
46 E
362
47 Y
363
48 M
364
49 P
365
50 Y
366
51 G
367
52 N
368
53 L
369
54 L
370
55 D
371
56 Y
372
57 L
373
58 R
374
59 E
375
60 Y
399
αE VI c.l VII VIII x
61 L
400
62 E
401
63 K
402
64 K
403
65 N
404
66 F
405
67 I
406
68 H
407
69 R
408
70 D
409
71 L
410
72 A
411
73 A
412
74 R
413
75 N
414
76 C
415
77 L
416
78 V
417
79 V
425
80 A
426
DFG a.l
81 D
427
82 F
428
83 G
429
84 L
430
85 S
431

Interaction pattern search
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Binding affinities
ChEMBL ID:CHEMBL261720
Bioaffinities: 7 records for 5 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensDual specificity protein kinase CLK37.57.57.5pIC501
Homo sapiensDual specificty protein kinase CLK18.18.18.1pIC501
Homo sapiensGlycogen synthase kinase-3 beta6.76.76.9pIC502
Homo sapiensInterferon-induced, double-stranded RNA-activated protein kinase5.85.85.8pIC501
Homo sapiensVascular endothelial growth factor receptor 27.57.57.5pIC502