PDB-code
| Kinase structure | |
| Kinase: | PDGFRA (PDGFRa) |
| Family: | PDGFR |
| Group: | TK |
| Species: | HUMAN |
| IUPHAR/BPS ID: | 1803 |
| PDB: | 6JOL |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2020-03-25 |
| Chain: | A |
| Orthosteric ligand: | STI |
 | |
| Structural information | |
| DFG conformation: | out |
| αC-helix conformation: | in |
| G-rich loop angle (distance): | 57.6° (18.1Å) |
| G-rich loop rotation: | 44.7° |
| Quality Score: | 8 |
| Resolution: | 1.9 Å |
| Missing Residues: | 0 |
| Missing Atoms: | 0 |
| Ligand binding mode | ||||
| Pockets | Subpockets | Waters | ||
| front gate back | BP-I-A BP-I-B BP-II-out BP-IV | Cluster I5 | Ligand Yes | Protein Yes |
| Pocket alignment | |
| Uniprot sequence: | RVLGSGAFGKVVEVAVKMLALMSELKIMTHLGLNIVNLLGAYIITEYCFYGDLVNYLHKFLASKNCVHRDLAARNVLLICDFGLA |
| Sequence structure: | RVLGSGAFGKVVEVAVKMLALMSELKIMTHLGLNIVNLLGAYIITEYCFYGDLVNYLHKFLASKNCVHRDLAARNVLLICDFGLA |
| 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 R 597 | 2 V 598 | 3 L 599 | 4 G 600 | 5 S 601 | 6 G 602 | 7 A 603 | 8 F 604 | 9 G 605 | 10 K 606 | 11 V 607 | 12 V 608 | 13 E 609 | 14 V 624 | 15 A 625 | 16 V 626 | 17 K 627 | 18 M 628 | 19 L 629 | 20 A 640 |
| • | • | • | • | • | |||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 L 641 | 22 M 642 | 23 S 643 | 24 E 644 | 25 L 645 | 26 K 646 | 27 I 647 | 28 M 648 | 29 T 649 | 30 H 650 | 31 L 651 | 32 G 652 | 33 L 655 | 34 N 656 | 35 I 657 | 36 V 658 | 37 N 659 | 38 L 660 | 39 L 661 | 40 G 662 |
| • | • | • | • | ||||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 A 663 | 42 Y 671 | 43 I 672 | 44 I 673 | 45 T 674 | 46 E 675 | 47 Y 676 | 48 C 677 | 49 F 678 | 50 Y 679 | 51 G 680 | 52 D 681 | 53 L 682 | 54 V 683 | 55 N 684 | 56 Y 685 | 57 L 686 | 58 H 687 | 59 K 688 | 60 F 808 |
| • | •• | •• | •• | • | |||||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 L 809 | 62 A 810 | 63 S 811 | 64 K 812 | 65 N 813 | 66 C 814 | 67 V 815 | 68 H 816 | 69 R 817 | 70 D 818 | 71 L 819 | 72 A 820 | 73 A 821 | 74 R 822 | 75 N 823 | 76 V 824 | 77 L 825 | 78 L 826 | 79 I 834 | 80 C 835 |
| • | •• | •• | • | • | • | ||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 836 | 82 F 837 | 83 G 838 | 84 L 839 | 85 A 840 | |||||||||||||||
| •• | •• | ||||||||||||||||||
Interaction pattern search
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