PDB-code
| Kinase structure | |
| Kinase: | KDR |
| Family: | VEGFR |
| Group: | TK |
| Species: | HUMAN |
| IUPHAR/BPS ID: | 1813 |
| PDB: | 3VNT |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2012-04-11 |
| PubMed: | 22376051 |
| Chain: | A |
| (Alternate) Model: | A |
| Orthosteric ligand: | 0JA |
 | |
| More entries for 3VNT | |||||
| 3VNT | Alternative model: | B | Chain: | A | |
| Structural information | |
| DFG conformation: | out |
| αC-helix conformation: | in |
| G-rich loop angle (distance): | 59.6° (18.2Å) |
| G-rich loop rotation: | 36.3° |
| Quality Score: | 7.6 |
| Resolution: | 1.64 Å |
| Missing Residues: | 0 |
| Missing Atoms: | 0 |
| Ligand binding mode | ||||
| Pockets | Subpockets | Waters | ||
| front gate back | BP-I-B BP-II-out BP-III | Cluster I1 | Ligand No | Protein Yes |
| Pocket alignment | |
| Uniprot sequence: | KPLGRGAFGQVIEVAVKMLALMSELKILIHIGLNVVNLLGAMVIVEFCKFGNLSTYLRSFLASRKCIHRDLAARNILLICDFGLA |
| Sequence structure: | KPLGRGAFGQVIEVAVKMLALMSELKILIHIGLNVVNLLGAMVIVEFCKFGNLSTYLRSFLASRKCIHRDLAARNILLICDFGLA |
| Ligand affinity | |
| ChEMBL ID: | CHEMBL2063743 |
| Bioaffinities: | 2 records for 2 kinases |
| Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
|---|---|---|---|---|---|---|
| Homo sapiens | Serine/threonine-protein kinase B-raf | 8.3 | 8.3 | 8.3 | pIC50 | 1 |
| Homo sapiens | Vascular endothelial growth factor receptor 2 | 8.6 | 8.6 | 8.6 | 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 K 838 | 2 P 839 | 3 L 840 | 4 G 841 | 5 R 842 | 6 G 843 | 7 A 844 | 8 F 845 | 9 G 846 | 10 Q 847 | 11 V 848 | 12 I 849 | 13 E 850 | 14 V 865 | 15 A 866 | 16 V 867 | 17 K 868 | 18 M 869 | 19 L 870 | 20 A 881 |
| • | • | • | • | ||||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 L 882 | 22 M 883 | 23 S 884 | 24 E 885 | 25 L 886 | 26 K 887 | 27 I 888 | 28 L 889 | 29 I 890 | 30 H 891 | 31 I 892 | 32 G 893 | 33 L 896 | 34 N 897 | 35 V 898 | 36 V 899 | 37 N 900 | 38 L 901 | 39 L 902 | 40 G 903 |
| •• | • | • | • | • | |||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 A 904 | 42 M 913 | 43 V 914 | 44 I 915 | 45 V 916 | 46 E 917 | 47 F 918 | 48 C 919 | 49 K 920 | 50 F 921 | 51 G 922 | 52 N 923 | 53 L 924 | 54 S 925 | 55 T 926 | 56 Y 927 | 57 L 928 | 58 R 929 | 59 S 930 | 60 F 1018 |
| • | • | • | •• | ••• | • | • | • | ||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 L 1019 | 62 A 1020 | 63 S 1021 | 64 R 1022 | 65 K 1023 | 66 C 1024 | 67 I 1025 | 68 H 1026 | 69 R 1027 | 70 D 1028 | 71 L 1029 | 72 A 1030 | 73 A 1031 | 74 R 1032 | 75 N 1033 | 76 I 1034 | 77 L 1035 | 78 L 1036 | 79 I 1044 | 80 C 1045 |
| • | • | • | • | • | |||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 1046 | 82 F 1047 | 83 G 1048 | 84 L 1049 | 85 A 1050 | |||||||||||||||
| •• | •• | ||||||||||||||||||
Interaction pattern search
Search KLIFS for kinase-ligand complexes with similar interaction patterns:
