PDB-code
| Kinase structure | |
| Kinase: | KDR |
| Family: | VEGFR |
| Group: | TK |
| Species: | HUMAN |
| IUPHAR/BPS ID: | 1813 |
| PDB: | 1Y6B |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2005-06-07 |
| PubMed: | 15743202 |
| Chain: | A |
| Orthosteric ligand: | AAX |
 | |
| Structural information | |
| DFG conformation: | out-like |
| αC-helix conformation: | in |
| G-rich loop angle (distance): | 64.1° (18.1Å) |
| G-rich loop rotation: | 65.7° |
| Quality Score: | 6 |
| Resolution: | 2.1 Å |
| Missing Residues: | 5 |
| Missing Atoms: | 0 |
| Ligand binding mode | ||||
| Pockets | Subpockets | Waters | ||
| front gate back | BP-I-A BP-I-B | Cluster I1 I2 | Ligand No Yes | Protein Yes Yes |
| Pocket alignment | |
| Uniprot sequence: | KPLGRGAFGQVIEVAVKMLALMSELKILIHIGLNVVNLLGAMVIVEFCKFGNLSTYLRSFLASRKCIHRDLAARNILLICDFGLA |
| Sequence structure: | KPLGRG__GQVIEVAVKMLALMSELKILIHIGLNVVNLLGAMVIVEFCKFGNLSTYLRSFLASRKCIHRDLAARNILLICDF___ |
| Ligand affinity | |
| Ligand not found in ChEMBL. | |
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 836 | 2 P 837 | 3 L 838 | 4 G 839 | 5 R 840 | 6 G 841 | 7 _ _ | 8 _ _ | 9 G 844 | 10 Q 845 | 11 V 846 | 12 I 847 | 13 E 848 | 14 V 863 | 15 A 864 | 16 V 865 | 17 K 866 | 18 M 867 | 19 L 868 | 20 A 879 |
| • | • | • | • | • | • | • | • | ||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 L 880 | 22 M 881 | 23 S 882 | 24 E 883 | 25 L 884 | 26 K 885 | 27 I 886 | 28 L 887 | 29 I 888 | 30 H 889 | 31 I 890 | 32 G 891 | 33 L 894 | 34 N 895 | 35 V 896 | 36 V 897 | 37 N 898 | 38 L 899 | 39 L 900 | 40 G 901 |
| •• | |||||||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 A 902 | 42 M 911 | 43 V 912 | 44 I 913 | 45 V 914 | 46 E 915 | 47 F 916 | 48 C 917 | 49 K 918 | 50 F 919 | 51 G 920 | 52 N 921 | 53 L 922 | 54 S 923 | 55 T 924 | 56 Y 925 | 57 L 926 | 58 R 927 | 59 S 928 | 60 F 1016 |
| • | • | • | •• | ••• | • | • | •• | ||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 L 1017 | 62 A 1018 | 63 S 1019 | 64 R 1020 | 65 K 1021 | 66 C 1022 | 67 I 1023 | 68 H 1024 | 69 R 1025 | 70 D 1026 | 71 L 1027 | 72 A 1028 | 73 A 1029 | 74 R 1030 | 75 N 1031 | 76 I 1032 | 77 L 1033 | 78 L 1034 | 79 I 1042 | 80 C 1043 |
| • | |||||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 1044 | 82 F 1045 | 83 _ _ | 84 _ _ | 85 _ _ | |||||||||||||||
| ••• | |||||||||||||||||||
Interaction pattern search
Search KLIFS for kinase-ligand complexes with similar interaction patterns:
