PDB-code
| Kinase structure | |
| Kinase: | NTRK3 (TRKC) |
| Family: | Trk |
| Group: | TK |
| Species: | HUMAN |
| IUPHAR/BPS ID: | 1819 |
| PDB: | 4YMJ |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2015-06-03 |
| PubMed: | 26005534 |
| Chain: | A |
| (Alternate) Model: | A |
| Orthosteric ligand: | 4EJ |
 | |
| More entries for 4YMJ | |||||
| 4YMJ | Alternative model: | A | Chain: | B | |
| 4YMJ | Alternative model: | B | Chain: | A | |
| 4YMJ | Alternative model: | B | Chain: | B | |
| Structural information | |
| DFG conformation: | out |
| αC-helix conformation: | out |
| G-rich loop angle (distance): | 61° (18.7Å) |
| G-rich loop rotation: | 38° |
| Quality Score: | 7.2 |
| Resolution: | 2 Å |
| Missing Residues: | 2 |
| Missing Atoms: | 12 |
| Ligand binding mode | ||||
| Pockets | Subpockets | Waters | ||
| front gate back | FP-II BP-I-B | Cluster I1 | Ligand No | Protein Yes |
| Pocket alignment | |
| Uniprot sequence: | RELGEGAFGKVFLVAVKALDFQREAELLTNLQEHIVKFYGVIMVFEYMKHGDLNKFLRAYLASQHFVHRDLATRNCLVIGDFGMS |
| Sequence structure: | RELGEGAFGKVFLVAVKALDFQREAELLTNLQEHIVKFYGVIMVFEYMKHGDLNKFLRAYLASQHFVHRDLATRNCLVIGDFG__ |
| Ligand affinity | |
| ChEMBL ID: | CHEMBL3582427 |
| Bioaffinities: | 33 records for 30 kinases |
| Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
|---|---|---|---|---|---|---|
| Homo sapiens | ALK tyrosine kinase receptor | 5.3 | 5.3 | 5.5 | pIC50 | 2 |
| Homo sapiens | Fibroblast growth factor receptor 3 | 5.4 | 5.4 | 5.4 | pIC50 | 1 |
| Homo sapiens | Fibroblast growth factor receptor 4 | 5.2 | 5.2 | 5.2 | pIC50 | 1 |
| Homo sapiens | Hepatocyte growth factor receptor | 5.3 | 5.3 | 5.3 | pIC50 | 1 |
| Homo sapiens | Insulin-like growth factor I receptor | 5.4 | 5.4 | 5.4 | pIC50 | 1 |
| Homo sapiens | Insulin receptor | 5.1 | 5.1 | 5.1 | pIC50 | 1 |
| Homo sapiens | Macrophage colony stimulating factor receptor | 5.5 | 5.5 | 5.5 | pIC50 | 1 |
| Homo sapiens | Macrophage-stimulating protein receptor | 5.2 | 5.2 | 5.2 | pIC50 | 1 |
| Homo sapiens | Nerve growth factor receptor Trk-A | 6.1 | 6.1 | 6.1 | pIC50 | 1 |
| Homo sapiens | Neurotrophic tyrosine kinase receptor type 2 | 6.6 | 6.6 | 7.1 | pIC50 | 2 |
| Homo sapiens | NT-3 growth factor receptor | 7 | 7 | 7 | pIC50 | 1 |
| Homo sapiens | Platelet-derived growth factor receptor beta | 5.7 | 5.7 | 5.7 | pIC50 | 1 |
| Homo sapiens | Proto-oncogene tyrosine-protein kinase MER | 5.3 | 5.3 | 5.3 | pIC50 | 1 |
| Homo sapiens | Proto-oncogene tyrosine-protein kinase ROS | 6.5 | 6.5 | 6.5 | pIC50 | 1 |
| Homo sapiens | Serine/threonine-protein kinase B-raf | 5.6 | 5.6 | 5.6 | pIC50 | 1 |
| Homo sapiens | Stem cell growth factor receptor | 5.7 | 5.7 | 5.7 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase ABL | 5.4 | 5.4 | 5.4 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase BMX | 5 | 5 | 5 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase FGR | 5.2 | 5.2 | 5.2 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase JAK2 | 5.3 | 5.3 | 5.3 | pIC50 | 2 |
| Homo sapiens | Tyrosine-protein kinase LCK | 5.7 | 5.7 | 5.7 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase Lyn | 5.1 | 5.1 | 5.1 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase receptor FLT3 | 6.1 | 6.1 | 6.1 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase receptor RET | 5.3 | 5.3 | 5.3 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase receptor Tie-1 | 5.3 | 5.3 | 5.3 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase SRC | 5.3 | 5.3 | 5.3 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase SYK | 5.4 | 5.4 | 5.4 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase ZAP-70 | 5.2 | 5.2 | 5.2 | pIC50 | 1 |
| Homo sapiens | Vascular endothelial growth factor receptor 1 | 5.5 | 5.5 | 5.5 | pIC50 | 1 |
| Homo sapiens | Vascular endothelial growth factor receptor 2 | 5.4 | 5.4 | 5.4 | pIC50 | 1 |
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 542 | 2 E 543 | 3 L 544 | 4 G 545 | 5 E 546 | 6 G 547 | 7 A 548 | 8 F 549 | 9 G 550 | 10 K 551 | 11 V 552 | 12 F 553 | 13 L 554 | 14 V 569 | 15 A 570 | 16 V 571 | 17 K 572 | 18 A 573 | 19 L 574 | 20 D 584 |
| • | • | • | • | • | |||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 F 585 | 22 Q 586 | 23 R 587 | 24 E 588 | 25 A 589 | 26 E 590 | 27 L 591 | 28 L 592 | 29 T 593 | 30 N 594 | 31 L 595 | 32 Q 596 | 33 E 598 | 34 H 599 | 35 I 600 | 36 V 601 | 37 K 602 | 38 F 603 | 39 Y 604 | 40 G 605 |
| • | |||||||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 V 606 | 42 I 614 | 43 M 615 | 44 V 616 | 45 F 617 | 46 E 618 | 47 Y 619 | 48 M 620 | 49 K 621 | 50 H 622 | 51 G 623 | 52 D 624 | 53 L 625 | 54 N 626 | 55 K 627 | 56 F 628 | 57 L 629 | 58 R 630 | 59 A 631 | 60 Y 669 |
| •• | • | •• | •• | • | |||||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 L 670 | 62 A 671 | 63 S 672 | 64 Q 673 | 65 H 674 | 66 F 675 | 67 V 676 | 68 H 677 | 69 R 678 | 70 D 679 | 71 L 680 | 72 A 681 | 73 T 682 | 74 R 683 | 75 N 684 | 76 C 685 | 77 L 686 | 78 V 687 | 79 I 695 | 80 G 696 |
| • | |||||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 697 | 82 F 698 | 83 G 699 | 84 _ _ | 85 _ _ | |||||||||||||||
| •• | |||||||||||||||||||
Interaction pattern search
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