5TOB - chain A | Protein tyrosine kinase 2 beta
Structure information
PDB:5TOB
PubMed:27876318
Release date:2017-11-29
Resolution:2.12 Å
 
Kinase:PTK2B (PYK2)
Family:FAK
Group:TK
Species:HUMAN
 
Quality Score:7.6
Missing Residues:2
Missing Atoms:16
DFG conformation:in
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:No
 
 
ASP rotation (xDFG.81) :91°
PHE rotation (xDFG.82) :10°
Activation loop position:-4.7Å
αC-helix position:17.9Å
 
G-rich loop angle:62.3°
G-rich loop distance:18.1Å
G-rich loop rotation:74.1°
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond protein
I11
H-bond ligand
H-bond protein
Binding pocket sequence
UniprotRILGEGFFGEVYEVAVKTCKFMSEAVIMKNLDPHIVKLIGIWIIMELYPYGELGHYLERYLESINCVHRDIAVRNILVLGDFGLS
Structure:RILGEGFFGEVYEVAVKTCKFMSEAVIMKNLDPHIVKLIGIWIIMELYPYGELGHYLERYLESINCVHRDIAVRNILVLGDFG__


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: YAM
Ligand Name: N-methyl-N-{3-[({2-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]-5-(trifluoromethyl)pyrimidin-4-yl}amino)methyl]pyridin-2-yl}methanesulfonamide

  • 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 R
429
2 I
430
3 L
431
4 G
432
5 E
433
6 G
434
7 F
435
8 F
436
9 G
437
10 E
438
11 V
439
12 Y
440
13 E
441
14 V
454
15 A
455
16 V
456
17 K
457
18 T
458
19 C
459
20 K
470
αC b.l IV
21 F
471
22 M
472
23 S
473
24 E
474
25 A
475
26 V
476
27 I
477
28 M
478
29 K
479
30 N
480
31 L
481
32 D
482
33 P
484
34 H
485
35 I
486
36 V
487
37 K
488
38 L
489
39 I
490
40 G
491
IV V GK hinge linker αD αE
41 I
492
42 W
499
43 I
500
44 I
501
45 M
502
46 E
503
47 L
504
48 Y
505
49 P
506
50 Y
507
51 G
508
52 E
509
53 L
510
54 G
511
55 H
512
56 Y
513
57 L
514
58 E
515
59 R
516
60 Y
539
αE VI c.l VII VIII x
61 L
540
62 E
541
63 S
542
64 I
543
65 N
544
66 C
545
67 V
546
68 H
547
69 R
548
70 D
549
71 I
550
72 A
551
73 V
552
74 R
553
75 N
554
76 I
555
77 L
556
78 V
557
79 L
565
80 G
566
DFG a.l
81 D
567
82 F
568
83 G
569
84 _
_
85 _
_

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:CHEMBL1084546
Bioaffinities: 162 records for 122 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiens3-phosphoinositide dependent protein kinase-1666pKi1
Homo sapiensALK tyrosine kinase receptor6.76.76.7pKi1
Homo sapiensAMP-activated protein kinase, alpha-1 subunit6.46.46.4pKi1
Homo sapiensBMP-2-inducible protein kinase5.55.55.5pKd1
Homo sapiensBR serine/threonine-protein kinase 15.35.35.3pKi1
Homo sapiensCaM kinase II delta5.45.45.4pKi1
Homo sapiensCaM kinase II gamma5.65.65.6pKi1
Homo sapiensCaM-kinase kinase beta6.56.56.5pKi1
Homo sapienscAMP-dependent protein kinase alpha-catalytic subunit6.86.86.8pKi1
Homo sapiensCasein kinase I gamma 15.45.45.4pKi1
Homo sapiensCasein kinase I gamma 25.85.85.8pKd1
Homo sapiensCasein kinase I gamma 25.45.45.4pKi1
Homo sapiensCasein kinase II alpha666pKi1
Homo sapiensCasein kinase II alpha (prime)666pKd1
Homo sapiensc-Jun N-terminal kinase 25.85.85.8pKi1
Homo sapiensc-Jun N-terminal kinase 36.66.66.6pKi1
Homo sapiensCyclin-dependent kinase 15.85.85.8pKd1
Homo sapiensCyclin-dependent kinase 17.27.27.2pKi1
Homo sapiensCyclin-dependent kinase 135.45.45.4pKd1
Homo sapiensCyclin-dependent kinase 2666pKd1
Homo sapiensCyclin-dependent kinase 27.17.17.1pKi1
Homo sapiensCyclin-dependent kinase 35.55.55.5pKd1
Homo sapiensCyclin-dependent kinase 56.36.36.3pKd1
Homo sapiensCyclin-dependent kinase 57.87.87.8pKi1
Homo sapiensCyclin-dependent kinase 75.95.95.9pKd1
Homo sapiensCyclin-dependent kinase 77.77.77.7pKi1
Homo sapiensCyclin-dependent kinase 95.95.95.9pKd1
Homo sapiensCyclin-dependent kinase 97.27.27.2pKi1
Homo sapiensDeath-associated protein kinase 3666pKi1
Homo sapiensDual specificity mitogen-activated protein kinase kinase 25.65.65.6pKi1
Homo sapiensDual specificity mitogen-activated protein kinase kinase 65.75.75.7pKd1
Homo sapiensDual specificity protein kinase CLK26.96.96.9pKi1
Homo sapiensDual specificity protein kinase CLK47.27.27.2pKi1
Homo sapiensDual specificty protein kinase CLK16.46.46.4pKd1
Homo sapiensEphrin type-A receptor 25.95.95.9pKi1
Homo sapiensFibroblast growth factor receptor 16.26.26.2pKi1
Homo sapiensFibroblast growth factor receptor 36.26.26.2pKi1
Homo sapiensFocal adhesion kinase 18.88.89pIC506
Homo sapiensFocal adhesion kinase 1999pKd1
Homo sapiensFocal adhesion kinase 19.29.29.2pKi1
Homo sapiensGlycogen synthase kinase-3 alpha6.16.16.1pKd1
Homo sapiensGlycogen synthase kinase-3 alpha7.17.17.1pKi1
Homo sapiensGlycogen synthase kinase-3 beta6.26.26.2pKd1
Homo sapiensGlycogen synthase kinase-3 beta777pKi1
Homo sapiensG protein-coupled receptor kinase 55.65.65.6pKi1
Homo sapiensHepatocyte growth factor receptor5.75.75.7pKd1
Homo sapiensHepatocyte growth factor receptor6.66.66.6pKi1
Homo sapiensHomeodomain-interacting protein kinase 26.76.76.7pKi1
Homo sapiensHomeodomain-interacting protein kinase 46.36.36.3pKi1
Homo sapiensInsulin-like growth factor I receptor6.16.16.1pKi1
Homo sapiensInsulin receptor6.36.36.3pKi1
Homo sapiensInterleukin-1 receptor-associated kinase 15.75.75.7pKi1
Homo sapiensInterleukin-1 receptor-associated kinase 45.65.65.6pKd1
Homo sapiensInterleukin-1 receptor-associated kinase 46.46.46.4pKi1
Homo sapiensLeucine-rich repeat serine/threonine-protein kinase 26.86.86.8pKi1
Homo sapiensLeukocyte tyrosine kinase receptor6.56.56.5pKi1
Homo sapiensMacrophage-stimulating protein receptor6.66.66.6pKi1
Homo sapiensMAP kinase ERK25.95.95.9pKd1
Homo sapiensMAP kinase ERK27.27.27.2pKi1
Homo sapiensMAP kinase p38 gamma5.65.65.6pKi1
Homo sapiensMAP/microtubule affinity-regulating kinase 25.65.65.6pKd1
Homo sapiensMAP/microtubule affinity-regulating kinase 26.56.56.5pKi1
Homo sapiensMAP/microtubule affinity-regulating kinase 46.96.96.9pKd1
Homo sapiensMAP/microtubule affinity-regulating kinase 47.37.37.3pKi1
Homo sapiensMaternal embryonic leucine zipper kinase5.85.85.8pKd1
Homo sapiensMaternal embryonic leucine zipper kinase7.17.17.1pKi1
Homo sapiensMisshapen-like kinase 16.26.26.2pKi1
Homo sapiensMitogen-activated protein kinase 155.85.85.8pKd1
Homo sapiensMitogen-activated protein kinase 75.55.55.5pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase 106.76.76.7pKi1
Homo sapiensMitogen-activated protein kinase kinase kinase 116.46.46.4pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 15.45.45.4pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 25.85.85.8pKi1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 46.66.66.6pKd1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 46.26.26.2pKi1
Homo sapiensMitogen-activated protein kinase kinase kinase kinase 56.96.96.9pKi1
Homo sapiensMixed lineage kinase 75.35.35.3pKi1
Homo sapiensNerve growth factor receptor Trk-A6.46.46.4pKi1
Homo sapiensNeurotrophic tyrosine kinase receptor type 27.47.47.4pKi1
Homo sapiensPlatelet-derived growth factor receptor beta666pKi1
Homo sapiensProtein kinase C delta4.94.94.9pKd1
Homo sapiensProtein kinase C delta5.85.85.8pKi1
Homo sapiensProtein kinase C gamma5.25.25.2pKi1
Homo sapiensProtein kinase C nu5.95.95.9pKi1
Homo sapiensProtein kinase C theta999pKd1
Homo sapiensProtein kinase C theta6.46.46.4pKi1
Homo sapiensProtein kinase N15.15.15.1pKd1
Homo sapiensProtein kinase N26.16.16.1pKi1
Homo sapiensProtein tyrosine kinase 2 beta7.97.97.9pIC503
Homo sapiensProtein tyrosine kinase 2 beta7.17.17.1pKd1
Homo sapiensProtein tyrosine kinase 2 beta8.58.58.5pKi1
Homo sapiensProto-oncogene tyrosine-protein kinase ROS7.97.97.9pKi1
Homo sapiensRho-associated protein kinase 15.75.75.7pKi1
Homo sapiensRho-associated protein kinase 25.75.75.7pKi1
Homo sapiensRibosomal protein S6 kinase 15.55.55.5pKi1
Homo sapiensRibosomal protein S6 kinase alpha 36.36.36.3pKi2
Homo sapiensSerine/threonine-protein kinase 116.26.26.2pKd1
Homo sapiensSerine/threonine-protein kinase 166.96.96.9pKd1
Homo sapiensSerine/threonine-protein kinase 17A5.95.95.9pKi1
Homo sapiensSerine/threonine-protein kinase 25.15.15.1pKd1
Homo sapiensSerine/threonine-protein kinase 26.66.66.6pKi1
Homo sapiensSerine/threonine-protein kinase Aurora-A6.26.26.2pKd1
Homo sapiensSerine/threonine-protein kinase Aurora-A6.96.96.9pKi1
Homo sapiensSerine/threonine-protein kinase Aurora-B666pKd1
Homo sapiensSerine/threonine-protein kinase Aurora-B7.27.27.2pKi1
Homo sapiensSerine/threonine-protein kinase Chk26.16.16.1pKi1
Homo sapiensSerine/threonine-protein kinase c-TAK15.65.65.6pKd1
Homo sapiensSerine/threonine-protein kinase c-TAK16.76.76.7pKi1
Homo sapiensSerine/threonine-protein kinase D25.75.75.7pKd1
Homo sapiensSerine/threonine-protein kinase D25.95.95.9pKi1
Homo sapiensSerine/threonine-protein kinase MRCK-A5.25.25.2pKi1
Homo sapiensSerine/threonine-protein kinase MST15.25.25.2pKd1
Homo sapiensSerine/threonine-protein kinase MST25.65.65.6pKd1
Homo sapiensSerine/threonine-protein kinase MST26.36.36.3pKi1
Homo sapiensSerine/threonine-protein kinase MST47.97.97.9pKd1
Homo sapiensSerine/threonine-protein kinase PAK 15.45.45.4pKi1
Homo sapiensSerine/threonine-protein kinase PAK 45.95.95.9pKd1
Homo sapiensSerine/threonine-protein kinase PAK 46.76.76.7pKi1
Homo sapiensSerine/threonine-protein kinase PCTAIRE-15.75.75.7pKd1
Homo sapiensSerine/threonine-protein kinase PCTAIRE-27.17.17.1pKd1
Homo sapiensSerine/threonine-protein kinase PLK46.26.26.2pKi1
Homo sapiensSerine/threonine-protein kinase PRKX6.16.16.1pKi1
Homo sapiensSerine/threonine-protein kinase Sgk25.65.65.6pKi1
Homo sapiensSerine/threonine-protein kinase SIK26.76.76.7pKi1
Homo sapiensSerine/threonine-protein kinase SRPK15.85.85.8pKi1
Homo sapiensSerine/threonine-protein kinase TAO16.76.76.7pKi1
Homo sapiensSerine/threonine-protein kinase TAO34.94.94.9pKd1
Homo sapiensSerine/threonine-protein kinase TBK15.75.75.7pKi1
Homo sapiensTestis-specific serine/threonine-protein kinase 15.85.85.8pKi1
Homo sapiensTyrosine kinase non-receptor protein 25.95.95.9pKi1
Homo sapiensTyrosine-protein kinase BLK6.46.46.4pKi1
Homo sapiensTyrosine-protein kinase BTK5.75.75.7pKi1
Homo sapiensTyrosine-protein kinase CTK777pKi1
Homo sapiensTyrosine-protein kinase FER6.16.16.1pKd1
Homo sapiensTyrosine-protein kinase FRK7.47.47.4pKi1
Homo sapiensTyrosine-protein kinase FYN5.75.75.7pKi1
Homo sapiensTyrosine-protein kinase HCK5.55.55.5pKi1
Homo sapiensTyrosine-protein kinase ITK/TSK7.17.17.1pKi1
Homo sapiensTyrosine-protein kinase JAK27.17.17.1pKi2
Homo sapiensTyrosine-protein kinase JAK3666pKi2
Homo sapiensTyrosine-protein kinase LCK6.36.36.3pKi1
Homo sapiensTyrosine-protein kinase Lyn777pKi1
Homo sapiensTyrosine-protein kinase receptor FLT35.95.95.9pKd1
Homo sapiensTyrosine-protein kinase receptor FLT36.46.46.4pKi1
Homo sapiensTyrosine-protein kinase receptor RET6.56.56.5pKi1
Homo sapiensTyrosine-protein kinase receptor UFO6.76.76.7pKi1
Homo sapiensTyrosine-protein kinase SRC6.36.36.3pKi1
Homo sapiensTyrosine-protein kinase TYK26.56.56.5pKi2
Homo sapiensVascular endothelial growth factor receptor 16.16.16.1pKi1
Homo sapiensVascular endothelial growth factor receptor 26.46.46.4pKi1
Homo sapiensVascular endothelial growth factor receptor 36.66.66.6pKi1