PDB-code
| Kinase structure | |
| Kinase: | SYK |
| Family: | Syk |
| Group: | TK |
| Species: | HUMAN |
| IUPHAR/BPS ID: | 2230 |
| PDB: | 1XBB |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2004-11-02 |
| PubMed: | 15507431 |
| Chain: | A |
| (Alternate) Model: | A |
| Orthosteric ligand: | STI |
 | |
| More entries for 1XBB | |||||
| 1XBB | Alternative model: | B | Chain: | A | |
| Structural information | |
| DFG conformation: | in |
| αC-helix conformation: | in |
| G-rich loop angle (distance): | 60.8° (18.9Å) |
| G-rich loop rotation: | 50.9° |
| Quality Score: | 8.1 |
| Resolution: | 1.57 Å |
| Missing Residues: | 0 |
| Missing Atoms: | 19 |
| Ligand binding mode | ||||
| Pockets | Subpockets | Waters | ||
| front | Cluster I2 I3 I4 I5 I10 | Ligand No Yes No Yes No | Protein Yes Yes Yes Yes Yes | |
| Pocket alignment | |
| Uniprot sequence: | KELGSGNFGTVKKVAVKILELLAEANVMQQLDPYIVRMIGIMLVMEMAELGPLNKYLQQYLEESNFVHRDLAARNVLLISDFGLS |
| Sequence structure: | KELGSGNFGTVKKVAVKILELLAEANVMQQLDPYIVRMIGIMLVMEMAELGPLNKYLQQYLEESNFVHRDLAARNVLLISDFGLS |
| Ligand affinity | |
| ChEMBL ID: | CHEMBL941 |
| Bioaffinities: | 228 records for 42 kinases |
| Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
|---|---|---|---|---|---|---|
| Homo sapiens | Cell division cycle 2-like protein kinase 6 | 5.3 | 5.3 | 5.3 | pKd | 2 |
| Homo sapiens | c-Jun N-terminal kinase 1 | 5.3 | 5.3 | 5.5 | pKd | 3 |
| Homo sapiens | c-Jun N-terminal kinase 2 | 5.3 | 5.3 | 5.3 | pKd | 1 |
| Homo sapiens | c-Jun N-terminal kinase 3 | 5.5 | 5.5 | 5.5 | pKd | 3 |
| Homo sapiens | c-Jun N-terminal kinase 3 | 6 | 6 | 6 | pKi | 1 |
| Homo sapiens | Discoidin domain-containing receptor 2 | 6.2 | 6.2 | 6.9 | pIC50 | 2 |
| Homo sapiens | Discoidin domain-containing receptor 2 | 7.8 | 7.8 | 7.8 | pKd | 2 |
| Homo sapiens | Dual specificity protein kinase CLK4 | 5.7 | 5.4 | 5.7 | pKd | 4 |
| Homo sapiens | Dual specificity protein kinase CLK4 | 5.9 | 5.9 | 5.9 | pKi | 1 |
| Homo sapiens | Dual specificty protein kinase CLK1 | 5.4 | 5.4 | 5.4 | pKd | 3 |
| Homo sapiens | Ephrin type-A receptor 8 | 5.9 | 5.7 | 5.9 | pKd | 3 |
| Homo sapiens | Epidermal growth factor receptor erbB1 | 5.1 | 5.1 | 5.1 | pKd | 2 |
| Homo sapiens | Epithelial discoidin domain-containing receptor 1 | 6.5 | 4.5 | 7.4 | pIC50 | 4 |
| Homo sapiens | Epithelial discoidin domain-containing receptor 1 | 9.2 | 9.2 | 9.2 | pKd | 2 |
| Homo sapiens | Homeodomain-interacting protein kinase 4 | 6 | 6 | 6 | pKd | 1 |
| Homo sapiens | Interleukin-1 receptor-associated kinase 1 | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Interleukin-1 receptor-associated kinase 1 | 5.1 | 5.1 | 5.1 | pKi | 1 |
| Homo sapiens | Macrophage colony stimulating factor receptor | 6 | 5.9 | 6.5 | pIC50 | 3 |
| Homo sapiens | Macrophage colony stimulating factor receptor | 7.7 | 7.7 | 8 | pKd | 2 |
| Homo sapiens | Macrophage colony stimulating factor receptor | 6.8 | 6.8 | 6.8 | pKi | 1 |
| Homo sapiens | MAP kinase p38 alpha | 4 | 4 | 4.9 | pIC50 | 2 |
| Homo sapiens | Maternal embryonic leucine zipper kinase | 5.7 | 5.7 | 5.7 | pKd | 2 |
| Homo sapiens | Mixed lineage kinase 7 | 5.6 | 5.6 | 5.6 | pKd | 2 |
| Homo sapiens | Platelet-derived growth factor receptor alpha | 7.1 | 7.1 | 7.1 | pEC50 | 1 |
| Homo sapiens | Platelet-derived growth factor receptor alpha | 7.1 | 6.8 | 8.7 | pIC50 | 6 |
| Homo sapiens | Platelet-derived growth factor receptor alpha | 7.5 | 7.5 | 7.5 | pKd | 2 |
| Homo sapiens | Platelet-derived growth factor receptor alpha | 6.8 | 6.8 | 6.8 | pKi | 1 |
| Homo sapiens | Platelet-derived growth factor receptor beta | 6.6 | 6.4 | 7.1 | pIC50 | 4 |
| Homo sapiens | Platelet-derived growth factor receptor beta | 7.9 | 7.6 | 7.9 | pKd | 3 |
| Homo sapiens | Platelet-derived growth factor receptor beta | 7.3 | 7.3 | 7.3 | pKi | 1 |
| Rattus norvegicus | Platelet-derived growth factor receptor beta | 6.8 | 6.8 | 6.8 | pIC50 | 1 |
| Homo sapiens | Serine/threonine-protein kinase 17A | 5.3 | 5.3 | 5.6 | pKd | 3 |
| Homo sapiens | Serine/threonine-protein kinase B-raf | 5.5 | 5.5 | 5.5 | pKd | 2 |
| Homo sapiens | Serine/threonine-protein kinase GAK | 6 | 5.4 | 6 | pKd | 3 |
| Homo sapiens | Serine/threonine-protein kinase PLK4 | 5.1 | 5.1 | 5.1 | pKd | 3 |
| Homo sapiens | Serine/threonine-protein kinase RAF | 5.8 | 5.8 | 5.8 | pKd | 2 |
| Homo sapiens | Serine/threonine-protein kinase TAO1 | 5.4 | 5.4 | 5.4 | pKi | 1 |
| Homo sapiens | Serine/threonine-protein kinase TNNI3K | 5.4 | 5.4 | 5.4 | pKd | 2 |
| Homo sapiens | Stem cell growth factor receptor | 7 | 7 | 7 | pEC50 | 1 |
| Homo sapiens | Stem cell growth factor receptor | 7 | 5 | 7.8 | pIC50 | 22 |
| Homo sapiens | Stem cell growth factor receptor | 7 | 5.5 | 7.9 | pKd | 16 |
| Homo sapiens | Tyrosine-protein kinase ABL | 6.7 | 4.1 | 7.7 | pIC50 | 32 |
| Homo sapiens | Tyrosine-protein kinase ABL | 7.4 | 5.2 | 9 | pKd | 26 |
| Homo sapiens | Tyrosine-protein kinase ABL | 7.4 | 5.2 | 7.9 | pKi | 6 |
| Mus musculus | Tyrosine-protein kinase ABL | 6.1 | 4.7 | 8 | pIC50 | 3 |
| Homo sapiens | Tyrosine-protein kinase ABL2 | 6.6 | 6.6 | 6.6 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase ABL2 | 8 | 6.3 | 8.2 | pKd | 5 |
| Homo sapiens | Tyrosine-protein kinase BLK | 6.3 | 6.3 | 6.3 | pKd | 2 |
| Homo sapiens | Tyrosine-protein kinase FGR | 5.6 | 5.6 | 5.6 | pKd | 2 |
| Homo sapiens | Tyrosine-protein kinase FRK | 5.8 | 5.5 | 5.8 | pKd | 3 |
| Homo sapiens | Tyrosine-protein kinase FRK | 6.5 | 6.5 | 6.5 | pKi | 1 |
| Homo sapiens | Tyrosine-protein kinase FYN | 5.5 | 5.3 | 5.5 | pKd | 3 |
| Homo sapiens | Tyrosine-protein kinase LCK | 6.5 | 6.5 | 6.8 | pIC50 | 3 |
| Homo sapiens | Tyrosine-protein kinase LCK | 7.4 | 7.2 | 7.4 | pKd | 3 |
| Homo sapiens | Tyrosine-protein kinase LCK | 6.5 | 6.5 | 6.5 | pKi | 1 |
| Homo sapiens | Tyrosine-protein kinase Lyn | 6.7 | 6.7 | 6.7 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase Lyn | 6.1 | 6.1 | 6.1 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase Lyn | 6.7 | 6.7 | 6.7 | pKi | 1 |
| Homo sapiens | Tyrosine-protein kinase receptor FLT3 | 5.2 | 5.2 | 5.2 | pKd | 1 |
| Gallus gallus | Tyrosine-protein kinase SRC | 5.6 | 5.6 | 5.6 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase SRC | 4.5 | 4.5 | 4.5 | pKi | 3 |
| Homo sapiens | Tyrosine-protein kinase SYK | 5.3 | 5.3 | 5.3 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase SYK | 5.3 | 5.3 | 5.3 | pKi | 2 |
| Homo sapiens | Tyrosine-protein kinase TYK2 | 5.1 | 5.1 | 5.1 | pKd | 2 |
| Homo sapiens | Vascular endothelial growth factor receptor 2 | 4.6 | 4.6 | 4.6 | pIC50 | 2 |
Kinase-ligand interaction pattern
• 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 K 375 | 2 E 376 | 3 L 377 | 4 G 378 | 5 S 379 | 6 G 380 | 7 N 381 | 8 F 382 | 9 G 383 | 10 T 384 | 11 V 385 | 12 K 386 | 13 K 387 | 14 V 399 | 15 A 400 | 16 V 401 | 17 K 402 | 18 I 403 | 19 L 404 | 20 E 416 |
| • | • | • | • | ||||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 L 417 | 22 L 418 | 23 A 419 | 24 E 420 | 25 A 421 | 26 N 422 | 27 V 423 | 28 M 424 | 29 Q 425 | 30 Q 426 | 31 L 427 | 32 D 428 | 33 P 430 | 34 Y 431 | 35 I 432 | 36 V 433 | 37 R 434 | 38 M 435 | 39 I 436 | 40 G 437 |
| • | |||||||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 I 438 | 42 M 445 | 43 L 446 | 44 V 447 | 45 M 448 | 46 E 449 | 47 M 450 | 48 A 451 | 49 E 452 | 50 L 453 | 51 G 454 | 52 P 455 | 53 L 456 | 54 N 457 | 55 K 458 | 56 Y 459 | 57 L 460 | 58 Q 461 | 59 Q 462 | 60 Y 484 |
| • | • | • | ••• | • | • | • | • | ||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 L 485 | 62 E 486 | 63 E 487 | 64 S 488 | 65 N 489 | 66 F 490 | 67 V 491 | 68 H 492 | 69 R 493 | 70 D 494 | 71 L 495 | 72 A 496 | 73 A 497 | 74 R 498 | 75 N 499 | 76 V 500 | 77 L 501 | 78 L 502 | 79 I 510 | 80 S 511 |
| • | • | ||||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 512 | 82 F 513 | 83 G 514 | 84 L 515 | 85 S 516 | |||||||||||||||
Interaction pattern search
Search KLIFS for kinase-ligand complexes with similar interaction patterns:
