4H1J - chain A | Protein tyrosine kinase 2 beta
Structure information
| PDB: | 4H1J |
| PubMed: | 23153798 |
| Release date: | 2012-11-28 |
| Resolution: | 2 Å |
| Kinase: | PTK2B (PYK2) |
| Family: | FAK |
| Group: | TK |
| Species: | HUMAN |
| Quality Score: | 7.6 |
| Missing Residues: | 0 |
| Missing Atoms: | 0 |
| DFG conformation: | out |
| αC-helix conformation: | in |
| Salt bridge KIII.17 and EαC.24: | Yes (2.8Å) |
| ASP rotation (xDFG.81) : | 180° |
| PHE rotation (xDFG.82) : | 159° |
| Activation loop position: | 1.6Å |
| αC-helix position: | 19Å |
| G-rich loop angle: | 67.8° |
| G-rich loop distance: | 20Å |
| G-rich loop rotation: | 81.8° |
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond protein
I4
H-bond protein
O1
H-bond ligand
O2
H-bond ligand
H-bond protein
Binding pocket sequence
| Uniprot | RILGEGFFGEVYEVAVKTCKFMSEAVIMKNLDPHIVKLIGIWIIMELYPYGELGHYLERYLESINCVHRDIAVRNILVLGDFGLS |
| Structure: | RILGEGFFGEVYEVAVKTCKFMSEAVIMKNLDPHIVKLIGIWIIMELYPYGELGHYLERYLESINCVHRDIAVRNILVLGDFGLS |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: 0YH
Ligand Name: 1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-[3-(4-methoxy-2-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
- 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 L 570 | 85 S 571 | |||||||||||||||
| ■▲ | ■♦ | ||||||||||||||||||
Binding affinities
ChEMBL ID:CHEMBL2207431Bioaffinities: 2 records for 2 kinase(s)
| Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
|---|---|---|---|---|---|---|
| Homo sapiens | Focal adhesion kinase 1 | 5.3 | 5.3 | 5.3 | pIC50 | 1 |
| Homo sapiens | Protein tyrosine kinase 2 beta | 5.9 | 5.9 | 5.9 | pIC50 | 1 |