4K9Y - chain A (model A) | Protein tyrosine kinase 2
Structure information
PDB: | 4K9Y |
PubMed: | 23973211 |
Release date: | 2013-09-11 |
Resolution: | 2 Å |
Kinase: | PTK2 (FAK) |
Family: | FAK |
Group: | TK |
Species: | HUMAN |
Quality Score: | 7.2 |
Missing Residues: | 0 |
Missing Atoms: | 0 |
DFG conformation: | out |
αC-helix conformation: | in |
Salt bridge KIII.17 and EαC.24: | Yes (2.7Å) |
ASP rotation (xDFG.81) : | 207° |
PHE rotation (xDFG.82) : | 201° |
Activation loop position: | 2.1Å |
αC-helix position: | 17.8Å |
G-rich loop angle: | 76.1° |
G-rich loop distance: | 22.4Å |
G-rich loop rotation: | 86.2° |
Other models from this PDB:
2D & 3D views
![The orthosteric binding pocket](KLIFS/final/HUMAN/FAK/4k9y_altA_chainA/image.png)
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond protein
I3
No H-bonds
O1
H-bond protein
O2
H-bond protein
Binding pocket sequence
Uniprot | RCIGEGQFGDVHQVAIKTCKFLQEALTMRQFDPHIVKLIGVWIIMELCTLGELRSFLQVYLESKRFVHRDIAARNVLVLGDFGLS |
Structure: | RCIGEGQFGDVHQVAIKTCKFLQEALTMRQFDPHIVKLIGVWIIMELCTLGELRSFLQVYLESKRFVHRDIAARNVLVLGDFGLS |
Modified residues
No modified residues identified.
Orthosteric ligand
![2D structure of the orthosteric ligand](KLIFS/final/HUMAN/FAK/4k9y_altA_chainA/ligand_v2.png)
Ligand HET-code: K9Y
Ligand Name: 1-[4-(6-amino-9H-purin-9-yl)phenyl]-3-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]urea
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- LABELS
- KLIFS residue #
- Amino Acid
- None
- COLORS
- Interaction types
- KLIFS (all res.)
- KLIFS (interacting res.)
- None
- OTHER
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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 R 426 | 2 C 427 | 3 I 428 | 4 G 429 | 5 E 430 | 6 G 431 | 7 Q 432 | 8 F 433 | 9 G 434 | 10 D 435 | 11 V 436 | 12 H 437 | 13 Q 438 | 14 V 451 | 15 A 452 | 16 I 453 | 17 K 454 | 18 T 455 | 19 C 456 | 20 K 467 |
■ | ■ | ■ | |||||||||||||||||
αC | b.l | IV | |||||||||||||||||
21 F 468 | 22 L 469 | 23 Q 470 | 24 E 471 | 25 A 472 | 26 L 473 | 27 T 474 | 28 M 475 | 29 R 476 | 30 Q 477 | 31 F 478 | 32 D 479 | 33 P 481 | 34 H 482 | 35 I 483 | 36 V 484 | 37 K 485 | 38 L 486 | 39 I 487 | 40 G 488 |
■▲ | ■ | ■ | ■ | ■ | ■ | ||||||||||||||
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 V 489 | 42 W 496 | 43 I 497 | 44 I 498 | 45 M 499 | 46 E 500 | 47 L 501 | 48 C 502 | 49 T 503 | 50 L 504 | 51 G 505 | 52 E 506 | 53 L 507 | 54 R 508 | 55 S 509 | 56 F 510 | 57 L 511 | 58 Q 512 | 59 V 513 | 60 Y 536 |
■ | ■ | ■ | ■▲▲ | ||||||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 L 537 | 62 E 538 | 63 S 539 | 64 K 540 | 65 R 541 | 66 F 542 | 67 V 543 | 68 H 544 | 69 R 545 | 70 D 546 | 71 I 547 | 72 A 548 | 73 A 549 | 74 R 550 | 75 N 551 | 76 V 552 | 77 L 553 | 78 V 554 | 79 L 562 | 80 G 563 |
■ | ■ | ■ | ■ | ■ | |||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 564 | 82 F 565 | 83 G 566 | 84 L 567 | 85 S 568 | |||||||||||||||
■▲ | ■♦ |
Binding affinities
ChEMBL ID:CHEMBL2425144Bioaffinities: 4 records for 2 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | Focal adhesion kinase 1 | 6.1 | 6.1 | 6.6 | pIC50 | 2 |
Homo sapiens | Focal adhesion kinase 1 | 7 | 7 | 7 | pKd | 1 |
Homo sapiens | Protein tyrosine kinase 2 beta | 6.4 | 6.4 | 6.4 | pIC50 | 1 |