6NPV - chain B (model A) | ABL proto-oncogene 1, non-receptor tyrosine kinase
Structure information
PDB:6NPV
PubMed:30689376
Release date:2019-03-13
Resolution:1.86 Å
 
Kinase:ABL1
Family:Abl
Group:TK
Species:HUMAN
 
Quality Score:8.9
Missing Residues:2
Missing Atoms:3
DFG conformation:out
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:Yes (2.8Å)
 
 
ASP rotation (xDFG.81) :189°
PHE rotation (xDFG.82) :179°
Activation loop position:2.3Å
αC-helix position:18.6Å
 
G-rich loop angle:62.6°
G-rich loop distance:18.5Å
G-rich loop rotation:15.4°
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
I4
H-bond protein
O1
H-bond ligand
Binding pocket sequence
UniprotHKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITEFMTYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFGLS
Structure:HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITEFMTYGNLLDYLREYLEKKNFIHRDLAARNCLVVADFG__


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: STI
Ligand Name: 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE

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  • 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 H
265
2 K
266
3 L
267
4 G
268
5 G
269
6 G
270
7 Q
271
8 Y
272
9 G
273
10 E
274
11 V
275
12 Y
276
13 E
277
14 V
287
15 A
288
16 V
289
17 K
290
18 T
291
19 L
292
20 E
301
αC b.l IV
21 F
302
22 L
303
23 K
304
24 E
305
25 A
306
26 A
307
27 V
308
28 M
309
29 K
310
30 E
311
31 I
312
32 K
313
33 P
315
34 N
316
35 L
317
36 V
318
37 Q
319
38 L
320
39 L
321
40 G
322
IV V GK hinge linker αD αE
41 V
323
42 Y
331
43 I
332
44 I
333
45 T
334
46 E
335
47 F
336
48 M
337
49 T
338
50 Y
339
51 G
340
52 N
341
53 L
342
54 L
343
55 D
344
56 Y
345
57 L
346
58 R
347
59 E
348
60 Y
372
αE VI c.l VII VIII x
61 L
373
62 E
374
63 K
375
64 K
376
65 N
377
66 F
378
67 I
379
68 H
380
69 R
381
70 D
382
71 L
383
72 A
384
73 A
385
74 R
386
75 N
387
76 C
388
77 L
389
78 V
390
79 V
398
80 A
399
DFG a.l
81 D
400
82 F
401
83 G
402
84 _
_
85 _
_

Interaction pattern search
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Binding affinities
ChEMBL ID:CHEMBL941
Bioaffinities: 254 records for 45 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensBreakpoint cluster region protein8.28.28.2pKd2
Homo sapiensCasein kinase II alpha (prime)5.45.45.4pKd1
Homo sapiensCell division cycle 2-like protein kinase 65.35.35.3pKd2
Homo sapiensc-Jun N-terminal kinase 15.35.35.5pKd3
Homo sapiensc-Jun N-terminal kinase 25.35.35.3pKd1
Homo sapiensc-Jun N-terminal kinase 35.55.55.5pKd3
Homo sapiensc-Jun N-terminal kinase 3666pKi1
Homo sapiensDiscoidin domain-containing receptor 26.26.26.9pIC502
Homo sapiensDiscoidin domain-containing receptor 27.86.77.8pKd3
Homo sapiensDual specificity protein kinase CLK45.75.45.7pKd4
Homo sapiensDual specificity protein kinase CLK45.95.95.9pKi1
Homo sapiensDual specificty protein kinase CLK15.45.45.4pKd3
Homo sapiensEphrin type-A receptor 85.95.75.9pKd3
Homo sapiensEpidermal growth factor receptor erbB15.15.15.1pKd2
Homo sapiensEpithelial discoidin domain-containing receptor 16.54.57.4pIC504
Homo sapiensEpithelial discoidin domain-containing receptor 19.17.79.2pKd4
Homo sapiensHomeodomain-interacting protein kinase 4666pKd1
Homo sapiensInterleukin-1 receptor-associated kinase 15.95.95.9pKd1
Homo sapiensInterleukin-1 receptor-associated kinase 15.15.15.1pKi1
Homo sapiensMacrophage colony stimulating factor receptor65.96.5pIC503
Homo sapiensMacrophage colony stimulating factor receptor87.78pKd3
Homo sapiensMacrophage colony stimulating factor receptor6.86.86.8pKi1
Homo sapiensMAP kinase p38 alpha444.9pIC502
Homo sapiensMAP kinase p38 alpha5.55.55.5pKd1
Homo sapiensMaternal embryonic leucine zipper kinase5.75.75.7pKd2
Homo sapiensMixed lineage kinase 75.65.65.6pKd2
Homo sapiensPhosphatidylinositol-5-phosphate 4-kinase type-2 gamma5.45.46.4pKd2
Homo sapiensPlatelet-derived growth factor receptor alpha7.17.17.1pEC501
Homo sapiensPlatelet-derived growth factor receptor alpha7.16.28.7pIC507
Homo sapiensPlatelet-derived growth factor receptor alpha7.57.57.5pKd2
Homo sapiensPlatelet-derived growth factor receptor alpha6.86.86.8pKi1
Homo sapiensPlatelet-derived growth factor receptor beta6.66.47.1pIC504
Homo sapiensPlatelet-derived growth factor receptor beta7.97.67.9pKd3
Homo sapiensPlatelet-derived growth factor receptor beta7.37.37.3pKi1
Rattus norvegicusPlatelet-derived growth factor receptor beta6.86.86.8pIC501
Homo sapiensSerine/threonine-protein kinase 17A5.35.35.6pKd3
Homo sapiensSerine/threonine-protein kinase B-raf5.55.55.5pKd2
Homo sapiensSerine/threonine-protein kinase GAK65.46pKd3
Homo sapiensSerine/threonine-protein kinase PLK45.15.15.1pKd3
Homo sapiensSerine/threonine-protein kinase RAF5.85.85.8pKd2
Homo sapiensSerine/threonine-protein kinase TAO15.45.45.4pKi1
Homo sapiensSerine/threonine-protein kinase TNNI3K5.45.45.4pKd2
Homo sapiensStem cell growth factor receptor777pEC501
Homo sapiensStem cell growth factor receptor757.8pIC5027
Homo sapiensStem cell growth factor receptor7.25.57.9pKd17
Homo sapiensTyrosine-protein kinase ABL6.74.17.7pIC5034
Homo sapiensTyrosine-protein kinase ABL7.45.29pKd28
Homo sapiensTyrosine-protein kinase ABL7.45.27.9pKi6
Mus musculusTyrosine-protein kinase ABL6.14.78pIC503
Homo sapiensTyrosine-protein kinase ABL26.66.66.6pIC501
Homo sapiensTyrosine-protein kinase ABL286.38.2pKd7
Homo sapiensTyrosine-protein kinase BLK6.36.36.3pKd2
Homo sapiensTyrosine-protein kinase FGR5.65.65.6pKd2
Homo sapiensTyrosine-protein kinase FRK5.85.55.8pKd3
Homo sapiensTyrosine-protein kinase FRK6.56.56.5pKi1
Homo sapiensTyrosine-protein kinase FYN5.55.35.5pKd3
Homo sapiensTyrosine-protein kinase LCK6.56.56.8pIC503
Homo sapiensTyrosine-protein kinase LCK7.47.27.4pKd4
Homo sapiensTyrosine-protein kinase LCK6.56.56.5pKi1
Homo sapiensTyrosine-protein kinase Lyn6.76.76.7pIC501
Homo sapiensTyrosine-protein kinase Lyn6.16.16.1pKd1
Homo sapiensTyrosine-protein kinase Lyn6.76.76.7pKi1
Homo sapiensTyrosine-protein kinase receptor FLT36.96.96.9pIC501
Homo sapiensTyrosine-protein kinase receptor FLT35.25.25.2pKd1
Gallus gallusTyrosine-protein kinase SRC5.65.65.6pIC501
Homo sapiensTyrosine-protein kinase SRC4.44.44.4pKd1
Homo sapiensTyrosine-protein kinase SRC4.54.54.5pKi3
Homo sapiensTyrosine-protein kinase SYK5.35.35.3pIC501
Homo sapiensTyrosine-protein kinase SYK5.35.35.3pKi2
Homo sapiensTyrosine-protein kinase TYK25.15.15.1pKd2
Homo sapiensVascular endothelial growth factor receptor 24.64.64.6pIC502
Allosteric ligand
2D structure of the allosteric ligand
Ligand HET-code: KWP
Ligand Name: ~{N}-[(4~{S})-2-(3,4-dichlorophenyl)-4-(2-hydroxyethyl)-3,4-dihydropyrazol-5-yl]pyridine-4-carboxamide

Binding affinities
Ligand not found in ChEMBL.