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
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
Uniprot | RILGEGFFGEVYEVAVKTCKFMSEAVIMKNLDPHIVKLIGIWIIMELYPYGELGHYLERYLESINCVHRDIAVRNILVLGDFGLS |
Structure: | RILGEGFFGEVYEVAVKTCKFMSEAVIMKNLDPHIVKLIGIWIIMELYPYGELGHYLERYLESINCVHRDIAVRNILVLGDFG__ |
Modified residues
No modified residues identified.
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
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- 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 _ _ | |||||||||||||||
Binding affinities
ChEMBL ID:CHEMBL1084546Bioaffinities: 162 records for 122 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | 3-phosphoinositide dependent protein kinase-1 | 6 | 6 | 6 | pKi | 1 |
Homo sapiens | ALK tyrosine kinase receptor | 6.7 | 6.7 | 6.7 | pKi | 1 |
Homo sapiens | AMP-activated protein kinase, alpha-1 subunit | 6.4 | 6.4 | 6.4 | pKi | 1 |
Homo sapiens | BMP-2-inducible protein kinase | 5.5 | 5.5 | 5.5 | pKd | 1 |
Homo sapiens | BR serine/threonine-protein kinase 1 | 5.3 | 5.3 | 5.3 | pKi | 1 |
Homo sapiens | CaM kinase II delta | 5.4 | 5.4 | 5.4 | pKi | 1 |
Homo sapiens | CaM kinase II gamma | 5.6 | 5.6 | 5.6 | pKi | 1 |
Homo sapiens | CaM-kinase kinase beta | 6.5 | 6.5 | 6.5 | pKi | 1 |
Homo sapiens | cAMP-dependent protein kinase alpha-catalytic subunit | 6.8 | 6.8 | 6.8 | pKi | 1 |
Homo sapiens | Casein kinase I gamma 1 | 5.4 | 5.4 | 5.4 | pKi | 1 |
Homo sapiens | Casein kinase I gamma 2 | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Casein kinase I gamma 2 | 5.4 | 5.4 | 5.4 | pKi | 1 |
Homo sapiens | Casein kinase II alpha | 6 | 6 | 6 | pKi | 1 |
Homo sapiens | Casein kinase II alpha (prime) | 6 | 6 | 6 | pKd | 1 |
Homo sapiens | c-Jun N-terminal kinase 2 | 5.8 | 5.8 | 5.8 | pKi | 1 |
Homo sapiens | c-Jun N-terminal kinase 3 | 6.6 | 6.6 | 6.6 | pKi | 1 |
Homo sapiens | Cyclin-dependent kinase 1 | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Cyclin-dependent kinase 1 | 7.2 | 7.2 | 7.2 | pKi | 1 |
Homo sapiens | Cyclin-dependent kinase 13 | 5.4 | 5.4 | 5.4 | pKd | 1 |
Homo sapiens | Cyclin-dependent kinase 2 | 6 | 6 | 6 | pKd | 1 |
Homo sapiens | Cyclin-dependent kinase 2 | 7.1 | 7.1 | 7.1 | pKi | 1 |
Homo sapiens | Cyclin-dependent kinase 3 | 5.5 | 5.5 | 5.5 | pKd | 1 |
Homo sapiens | Cyclin-dependent kinase 5 | 6.3 | 6.3 | 6.3 | pKd | 1 |
Homo sapiens | Cyclin-dependent kinase 5 | 7.8 | 7.8 | 7.8 | pKi | 1 |
Homo sapiens | Cyclin-dependent kinase 7 | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Cyclin-dependent kinase 7 | 7.7 | 7.7 | 7.7 | pKi | 1 |
Homo sapiens | Cyclin-dependent kinase 9 | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Cyclin-dependent kinase 9 | 7.2 | 7.2 | 7.2 | pKi | 1 |
Homo sapiens | Death-associated protein kinase 3 | 6 | 6 | 6 | pKi | 1 |
Homo sapiens | Dual specificity mitogen-activated protein kinase kinase 2 | 5.6 | 5.6 | 5.6 | pKi | 1 |
Homo sapiens | Dual specificity mitogen-activated protein kinase kinase 6 | 5.7 | 5.7 | 5.7 | pKd | 1 |
Homo sapiens | Dual specificity protein kinase CLK2 | 6.9 | 6.9 | 6.9 | pKi | 1 |
Homo sapiens | Dual specificity protein kinase CLK4 | 7.2 | 7.2 | 7.2 | pKi | 1 |
Homo sapiens | Dual specificty protein kinase CLK1 | 6.4 | 6.4 | 6.4 | pKd | 1 |
Homo sapiens | Ephrin type-A receptor 2 | 5.9 | 5.9 | 5.9 | pKi | 1 |
Homo sapiens | Fibroblast growth factor receptor 1 | 6.2 | 6.2 | 6.2 | pKi | 1 |
Homo sapiens | Fibroblast growth factor receptor 3 | 6.2 | 6.2 | 6.2 | pKi | 1 |
Homo sapiens | Focal adhesion kinase 1 | 8.8 | 8.8 | 9 | pIC50 | 6 |
Homo sapiens | Focal adhesion kinase 1 | 9 | 9 | 9 | pKd | 1 |
Homo sapiens | Focal adhesion kinase 1 | 9.2 | 9.2 | 9.2 | pKi | 1 |
Homo sapiens | Glycogen synthase kinase-3 alpha | 6.1 | 6.1 | 6.1 | pKd | 1 |
Homo sapiens | Glycogen synthase kinase-3 alpha | 7.1 | 7.1 | 7.1 | pKi | 1 |
Homo sapiens | Glycogen synthase kinase-3 beta | 6.2 | 6.2 | 6.2 | pKd | 1 |
Homo sapiens | Glycogen synthase kinase-3 beta | 7 | 7 | 7 | pKi | 1 |
Homo sapiens | G protein-coupled receptor kinase 5 | 5.6 | 5.6 | 5.6 | pKi | 1 |
Homo sapiens | Hepatocyte growth factor receptor | 5.7 | 5.7 | 5.7 | pKd | 1 |
Homo sapiens | Hepatocyte growth factor receptor | 6.6 | 6.6 | 6.6 | pKi | 1 |
Homo sapiens | Homeodomain-interacting protein kinase 2 | 6.7 | 6.7 | 6.7 | pKi | 1 |
Homo sapiens | Homeodomain-interacting protein kinase 4 | 6.3 | 6.3 | 6.3 | pKi | 1 |
Homo sapiens | Insulin-like growth factor I receptor | 6.1 | 6.1 | 6.1 | pKi | 1 |
Homo sapiens | Insulin receptor | 6.3 | 6.3 | 6.3 | pKi | 1 |
Homo sapiens | Interleukin-1 receptor-associated kinase 1 | 5.7 | 5.7 | 5.7 | pKi | 1 |
Homo sapiens | Interleukin-1 receptor-associated kinase 4 | 5.6 | 5.6 | 5.6 | pKd | 1 |
Homo sapiens | Interleukin-1 receptor-associated kinase 4 | 6.4 | 6.4 | 6.4 | pKi | 1 |
Homo sapiens | Leucine-rich repeat serine/threonine-protein kinase 2 | 6.8 | 6.8 | 6.8 | pKi | 1 |
Homo sapiens | Leukocyte tyrosine kinase receptor | 6.5 | 6.5 | 6.5 | pKi | 1 |
Homo sapiens | Macrophage-stimulating protein receptor | 6.6 | 6.6 | 6.6 | pKi | 1 |
Homo sapiens | MAP kinase ERK2 | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | MAP kinase ERK2 | 7.2 | 7.2 | 7.2 | pKi | 1 |
Homo sapiens | MAP kinase p38 gamma | 5.6 | 5.6 | 5.6 | pKi | 1 |
Homo sapiens | MAP/microtubule affinity-regulating kinase 2 | 5.6 | 5.6 | 5.6 | pKd | 1 |
Homo sapiens | MAP/microtubule affinity-regulating kinase 2 | 6.5 | 6.5 | 6.5 | pKi | 1 |
Homo sapiens | MAP/microtubule affinity-regulating kinase 4 | 6.9 | 6.9 | 6.9 | pKd | 1 |
Homo sapiens | MAP/microtubule affinity-regulating kinase 4 | 7.3 | 7.3 | 7.3 | pKi | 1 |
Homo sapiens | Maternal embryonic leucine zipper kinase | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Maternal embryonic leucine zipper kinase | 7.1 | 7.1 | 7.1 | pKi | 1 |
Homo sapiens | Misshapen-like kinase 1 | 6.2 | 6.2 | 6.2 | pKi | 1 |
Homo sapiens | Mitogen-activated protein kinase 15 | 5.8 | 5.8 | 5.8 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase 7 | 5.5 | 5.5 | 5.5 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase 10 | 6.7 | 6.7 | 6.7 | pKi | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase 11 | 6.4 | 6.4 | 6.4 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 1 | 5.4 | 5.4 | 5.4 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 2 | 5.8 | 5.8 | 5.8 | pKi | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 4 | 6.6 | 6.6 | 6.6 | pKd | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 4 | 6.2 | 6.2 | 6.2 | pKi | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 5 | 6.9 | 6.9 | 6.9 | pKi | 1 |
Homo sapiens | Mixed lineage kinase 7 | 5.3 | 5.3 | 5.3 | pKi | 1 |
Homo sapiens | Nerve growth factor receptor Trk-A | 6.4 | 6.4 | 6.4 | pKi | 1 |
Homo sapiens | Neurotrophic tyrosine kinase receptor type 2 | 7.4 | 7.4 | 7.4 | pKi | 1 |
Homo sapiens | Platelet-derived growth factor receptor beta | 6 | 6 | 6 | pKi | 1 |
Homo sapiens | Protein kinase C delta | 4.9 | 4.9 | 4.9 | pKd | 1 |
Homo sapiens | Protein kinase C delta | 5.8 | 5.8 | 5.8 | pKi | 1 |
Homo sapiens | Protein kinase C gamma | 5.2 | 5.2 | 5.2 | pKi | 1 |
Homo sapiens | Protein kinase C nu | 5.9 | 5.9 | 5.9 | pKi | 1 |
Homo sapiens | Protein kinase C theta | 9 | 9 | 9 | pKd | 1 |
Homo sapiens | Protein kinase C theta | 6.4 | 6.4 | 6.4 | pKi | 1 |
Homo sapiens | Protein kinase N1 | 5.1 | 5.1 | 5.1 | pKd | 1 |
Homo sapiens | Protein kinase N2 | 6.1 | 6.1 | 6.1 | pKi | 1 |
Homo sapiens | Protein tyrosine kinase 2 beta | 7.9 | 7.9 | 7.9 | pIC50 | 3 |
Homo sapiens | Protein tyrosine kinase 2 beta | 7.1 | 7.1 | 7.1 | pKd | 1 |
Homo sapiens | Protein tyrosine kinase 2 beta | 8.5 | 8.5 | 8.5 | pKi | 1 |
Homo sapiens | Proto-oncogene tyrosine-protein kinase ROS | 7.9 | 7.9 | 7.9 | pKi | 1 |
Homo sapiens | Rho-associated protein kinase 1 | 5.7 | 5.7 | 5.7 | pKi | 1 |
Homo sapiens | Rho-associated protein kinase 2 | 5.7 | 5.7 | 5.7 | pKi | 1 |
Homo sapiens | Ribosomal protein S6 kinase 1 | 5.5 | 5.5 | 5.5 | pKi | 1 |
Homo sapiens | Ribosomal protein S6 kinase alpha 3 | 6.3 | 6.3 | 6.3 | pKi | 2 |
Homo sapiens | Serine/threonine-protein kinase 11 | 6.2 | 6.2 | 6.2 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase 16 | 6.9 | 6.9 | 6.9 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase 17A | 5.9 | 5.9 | 5.9 | pKi | 1 |
Homo sapiens | Serine/threonine-protein kinase 2 | 5.1 | 5.1 | 5.1 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase 2 | 6.6 | 6.6 | 6.6 | pKi | 1 |
Homo sapiens | Serine/threonine-protein kinase Aurora-A | 6.2 | 6.2 | 6.2 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase Aurora-A | 6.9 | 6.9 | 6.9 | pKi | 1 |
Homo sapiens | Serine/threonine-protein kinase Aurora-B | 6 | 6 | 6 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase Aurora-B | 7.2 | 7.2 | 7.2 | pKi | 1 |
Homo sapiens | Serine/threonine-protein kinase Chk2 | 6.1 | 6.1 | 6.1 | pKi | 1 |
Homo sapiens | Serine/threonine-protein kinase c-TAK1 | 5.6 | 5.6 | 5.6 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase c-TAK1 | 6.7 | 6.7 | 6.7 | pKi | 1 |
Homo sapiens | Serine/threonine-protein kinase D2 | 5.7 | 5.7 | 5.7 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase D2 | 5.9 | 5.9 | 5.9 | pKi | 1 |
Homo sapiens | Serine/threonine-protein kinase MRCK-A | 5.2 | 5.2 | 5.2 | pKi | 1 |
Homo sapiens | Serine/threonine-protein kinase MST1 | 5.2 | 5.2 | 5.2 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase MST2 | 5.6 | 5.6 | 5.6 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase MST2 | 6.3 | 6.3 | 6.3 | pKi | 1 |
Homo sapiens | Serine/threonine-protein kinase MST4 | 7.9 | 7.9 | 7.9 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase PAK 1 | 5.4 | 5.4 | 5.4 | pKi | 1 |
Homo sapiens | Serine/threonine-protein kinase PAK 4 | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase PAK 4 | 6.7 | 6.7 | 6.7 | pKi | 1 |
Homo sapiens | Serine/threonine-protein kinase PCTAIRE-1 | 5.7 | 5.7 | 5.7 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase PCTAIRE-2 | 7.1 | 7.1 | 7.1 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase PLK4 | 6.2 | 6.2 | 6.2 | pKi | 1 |
Homo sapiens | Serine/threonine-protein kinase PRKX | 6.1 | 6.1 | 6.1 | pKi | 1 |
Homo sapiens | Serine/threonine-protein kinase Sgk2 | 5.6 | 5.6 | 5.6 | pKi | 1 |
Homo sapiens | Serine/threonine-protein kinase SIK2 | 6.7 | 6.7 | 6.7 | pKi | 1 |
Homo sapiens | Serine/threonine-protein kinase SRPK1 | 5.8 | 5.8 | 5.8 | pKi | 1 |
Homo sapiens | Serine/threonine-protein kinase TAO1 | 6.7 | 6.7 | 6.7 | pKi | 1 |
Homo sapiens | Serine/threonine-protein kinase TAO3 | 4.9 | 4.9 | 4.9 | pKd | 1 |
Homo sapiens | Serine/threonine-protein kinase TBK1 | 5.7 | 5.7 | 5.7 | pKi | 1 |
Homo sapiens | Testis-specific serine/threonine-protein kinase 1 | 5.8 | 5.8 | 5.8 | pKi | 1 |
Homo sapiens | Tyrosine kinase non-receptor protein 2 | 5.9 | 5.9 | 5.9 | pKi | 1 |
Homo sapiens | Tyrosine-protein kinase BLK | 6.4 | 6.4 | 6.4 | pKi | 1 |
Homo sapiens | Tyrosine-protein kinase BTK | 5.7 | 5.7 | 5.7 | pKi | 1 |
Homo sapiens | Tyrosine-protein kinase CTK | 7 | 7 | 7 | pKi | 1 |
Homo sapiens | Tyrosine-protein kinase FER | 6.1 | 6.1 | 6.1 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase FRK | 7.4 | 7.4 | 7.4 | pKi | 1 |
Homo sapiens | Tyrosine-protein kinase FYN | 5.7 | 5.7 | 5.7 | pKi | 1 |
Homo sapiens | Tyrosine-protein kinase HCK | 5.5 | 5.5 | 5.5 | pKi | 1 |
Homo sapiens | Tyrosine-protein kinase ITK/TSK | 7.1 | 7.1 | 7.1 | pKi | 1 |
Homo sapiens | Tyrosine-protein kinase JAK2 | 7.1 | 7.1 | 7.1 | pKi | 2 |
Homo sapiens | Tyrosine-protein kinase JAK3 | 6 | 6 | 6 | pKi | 2 |
Homo sapiens | Tyrosine-protein kinase LCK | 6.3 | 6.3 | 6.3 | pKi | 1 |
Homo sapiens | Tyrosine-protein kinase Lyn | 7 | 7 | 7 | pKi | 1 |
Homo sapiens | Tyrosine-protein kinase receptor FLT3 | 5.9 | 5.9 | 5.9 | pKd | 1 |
Homo sapiens | Tyrosine-protein kinase receptor FLT3 | 6.4 | 6.4 | 6.4 | pKi | 1 |
Homo sapiens | Tyrosine-protein kinase receptor RET | 6.5 | 6.5 | 6.5 | pKi | 1 |
Homo sapiens | Tyrosine-protein kinase receptor UFO | 6.7 | 6.7 | 6.7 | pKi | 1 |
Homo sapiens | Tyrosine-protein kinase SRC | 6.3 | 6.3 | 6.3 | pKi | 1 |
Homo sapiens | Tyrosine-protein kinase TYK2 | 6.5 | 6.5 | 6.5 | pKi | 2 |
Homo sapiens | Vascular endothelial growth factor receptor 1 | 6.1 | 6.1 | 6.1 | pKi | 1 |
Homo sapiens | Vascular endothelial growth factor receptor 2 | 6.4 | 6.4 | 6.4 | pKi | 1 |
Homo sapiens | Vascular endothelial growth factor receptor 3 | 6.6 | 6.6 | 6.6 | pKi | 1 |