3CS9 - chain D (model A) | ABL proto-oncogene 1, non-receptor tyrosine kinase
Structure information
PDB:3CS9
PubMed:15710326
Release date:2008-04-22
Resolution:2.21 Å
 
Kinase:ABL1
Family:Abl
Group:TK
Species:HUMAN
 
Quality Score:9.2
Missing Residues:0
Missing Atoms:4
DFG conformation:out
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:Yes (2.7Å)
 
 
ASP rotation (xDFG.81) :185°
PHE rotation (xDFG.82) :176°
Activation loop position:2.4Å
αC-helix position:18.5Å
 
G-rich loop angle:64.8°
G-rich loop distance:19Å
G-rich loop rotation:11°
Other models from this PDB:
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
O1
H-bond ligand
Binding pocket sequence
UniprotHKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITEFMTYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS
Structure:HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITEFMTYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: NIL
Ligand Name: Nilotinib

  • Download image
  • LABELS
  • KLIFS residue #
  • Amino Acid
  • None
  • COLORS
  • Interaction types
  • KLIFS (all res.)
  • KLIFS (interacting res.)
  • None
  • OTHER
  • Show/hide non-interacting res.
  • En/disable resizing interacting res.
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
246
2 K
247
3 L
248
4 G
249
5 G
250
6 G
251
7 Q
252
8 Y
253
9 G
254
10 E
255
11 V
256
12 Y
257
13 E
258
14 V
268
15 A
269
16 V
270
17 K
271
18 T
272
19 L
273
20 E
282
αC b.l IV
21 F
283
22 L
284
23 K
285
24 E
286
25 A
287
26 A
288
27 V
289
28 M
290
29 K
291
30 E
292
31 I
293
32 K
294
33 P
296
34 N
297
35 L
298
36 V
299
37 Q
300
38 L
301
39 L
302
40 G
303
IV V GK hinge linker αD αE
41 V
304
42 Y
312
43 I
313
44 I
314
45 T
315
46 E
316
47 F
317
48 M
318
49 T
319
50 Y
320
51 G
321
52 N
322
53 L
323
54 L
324
55 D
325
56 Y
326
57 L
327
58 R
328
59 E
329
60 Y
353
αE VI c.l VII VIII x
61 L
354
62 E
355
63 K
356
64 K
357
65 N
358
66 F
359
67 I
360
68 H
361
69 R
362
70 D
363
71 L
364
72 A
365
73 A
366
74 R
367
75 N
368
76 C
369
77 L
370
78 V
371
79 V
379
80 A
380
DFG a.l
81 D
381
82 F
382
83 G
383
84 L
384
85 S
385

Interaction pattern search
Search KLIFS for kinase-ligand complexes with similar interaction patterns:
Specify the minimum similarity (0.00 no similarity, 1.00 identical)
Binding affinities
ChEMBL ID:CHEMBL255863
Bioaffinities: 136 records for 59 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensBreakpoint cluster region protein6.26.26.2pKd2
Plasmodium falciparumCalcium-dependent protein kinase 16.16.16.1pKd1
Homo sapiensc-Jun N-terminal kinase 16.46.46.4pKd1
Homo sapiensc-Jun N-terminal kinase 25.25.25.2pKd1
Homo sapiensc-Jun N-terminal kinase 35.75.75.7pKd1
Homo sapiensDiscoidin domain-containing receptor 27.878.7pIC505
Homo sapiensDiscoidin domain-containing receptor 27.56.58.2pKd5
Homo sapiensDual specificity mitogen-activated protein kinase kinase 56.76.76.7pKd1
Homo sapiensDual specificity protein kinase CLK45.25.25.2pKd1
Homo sapiensDual specificty protein kinase CLK15.75.75.7pKd2
Homo sapiensEphrin type-A receptor 16.26.26.2pKd1
Homo sapiensEphrin type-A receptor 26.16.16.6pKd2
Homo sapiensEphrin type-A receptor 3777pKd1
Homo sapiensEphrin type-A receptor 46.56.56.5pKd1
Homo sapiensEphrin type-A receptor 55.75.75.7pKd1
Homo sapiensEphrin type-A receptor 66.26.26.2pKd1
Homo sapiensEphrin type-A receptor 87.47.47.4pKd1
Homo sapiensEphrin type-B receptor 15.95.95.9pKd1
Homo sapiensEphrin type-B receptor 26.26.26.2pKd1
Homo sapiensEphrin type-B receptor 3666pKd1
Homo sapiensEphrin type-B receptor 46.16.16.1pKd1
Homo sapiensEphrin type-B receptor 66.36.36.3pKd1
Homo sapiensEpithelial discoidin domain-containing receptor 17.57.48.4pIC503
Homo sapiensEpithelial discoidin domain-containing receptor 16.96.99pKd2
Homo sapiensMacrophage colony stimulating factor receptor6.26.26.2pIC501
Homo sapiensMacrophage colony stimulating factor receptor7.47.47.4pKd1
Homo sapiensMAP kinase p38 alpha6.366.3pKd3
Homo sapiensMAP kinase p38 beta5.45.47.4pKd2
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 16.16.16.1pKd1
Homo sapiensMixed lineage kinase 7668pKd2
Homo sapiensNeurotrophic tyrosine kinase receptor type 26.36.36.3pKd1
Homo sapiensNT-3 growth factor receptor6.26.26.2pKd1
Homo sapiensPhosphatidylinositol-5-phosphate 4-kinase type-2 gamma5.15.15.1pKd1
Homo sapiensPhosphorylase kinase gamma subunit 26.56.56.5pKd1
Homo sapiensPlatelet-derived growth factor receptor alpha7.27.27.2pIC501
Homo sapiensPlatelet-derived growth factor receptor alpha6.86.87.1pKd2
Homo sapiensPlatelet-derived growth factor receptor beta7.27.27.6pIC503
Homo sapiensPlatelet-derived growth factor receptor beta7.17.17.8pKd2
Homo sapiensReceptor-interacting serine/threonine-protein kinase 35.95.95.9pKd1
Homo sapiensSerine/threonine-protein kinase 105.25.25.2pKd1
Homo sapiensSerine/threonine-protein kinase B-raf5.85.86.2pKd2
Homo sapiensSerine/threonine-protein kinase ILK-17.77.77.7pKd1
Homo sapiensSerine/threonine-protein kinase MRCK beta666pKd1
Homo sapiensSerine/threonine-protein kinase RAF666pIC501
Homo sapiensSerine/threonine-protein kinase RAF5.45.45.4pKd1
Homo sapiensSerine/threonine-protein kinase TAO15.35.35.3pKd1
Homo sapiensSerine/threonine-protein kinase TAO35.85.85.8pKd1
Homo sapiensSerine/threonine-protein kinase TNNI3K6.46.46.4pKd1
Homo sapiensStem cell growth factor receptor6.86.77.8pIC504
Homo sapiensStem cell growth factor receptor7.36.17.8pKd9
Homo sapiensTyrosine-protein kinase ABL7.66.28.9pIC5012
Homo sapiensTyrosine-protein kinase ABL7.96.28.4pKd17
Homo sapiensTyrosine-protein kinase ABL26.56.57.6pKd2
Homo sapiensTyrosine-protein kinase BLK6.36.36.3pKd1
Homo sapiensTyrosine-protein kinase CSK5.65.65.6pKd1
Homo sapiensTyrosine-protein kinase FGR6.56.56.5pKd1
Homo sapiensTyrosine-protein kinase FRK6.36.37.1pKd2
Homo sapiensTyrosine-protein kinase FYN5.85.85.8pKd1
Homo sapiensTyrosine-protein kinase HCK6.46.46.4pKd1
Homo sapiensTyrosine-protein kinase LCK777pIC501
Homo sapiensTyrosine-protein kinase LCK7.37.37.3pKd1
Homo sapiensTyrosine-protein kinase Lyn5.95.95.9pIC501
Homo sapiensTyrosine-protein kinase Lyn5.85.87pKd2
Homo sapiensTyrosine-protein kinase receptor FLT3555pIC501
Homo sapiensTyrosine-protein kinase receptor FLT34.44.44.4pKd1
Homo sapiensTyrosine-protein kinase receptor RET666.1pKd2
Homo sapiensTyrosine-protein kinase receptor Tie-1666pKd1
Homo sapiensTyrosine-protein kinase SRC5.75.75.7pIC501
Homo sapiensTyrosine-protein kinase SRC5.75.75.7pKd1
Homo sapiensTyrosine-protein kinase TIE-2666pKd1
Homo sapiensTyrosine-protein kinase YES666pKd1