PDB-code
| Kinase structure | |
| Kinase: | KDR |
| Family: | VEGFR |
| Group: | TK |
| Species: | HUMAN |
| IUPHAR/BPS ID: | 1813 |
| PDB: | 5EW3 |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2015-12-16 |
| PubMed: | 15023347 |
| Chain: | A |
| Orthosteric ligand: | 5T2 |
 | |
| More entries for 5EW3 | |||
| 5EW3 | Chain: | B | |
| Structural information | |
| DFG conformation: | out |
| αC-helix conformation: | in |
| G-rich loop angle (distance): | 60.6° (18.8Å) |
| G-rich loop rotation: | 63.2° |
| Quality Score: | 7.6 |
| Resolution: | 2.5 Å |
| Missing Residues: | 1 |
| Missing Atoms: | 0 |
| Ligand binding mode | ||||
| Pockets | Subpockets | |||
| front gate back | BP-I-A BP-I-B BP-II-out BP-III | |||
| Pocket alignment | |
| Uniprot sequence: | KPLGRGAFGQVIEVAVKMLALMSELKILIHIGLNVVNLLGAMVIVEFCKFGNLSTYLRSFLASRKCIHRDLAARNILLICDFGLA |
| Sequence structure: | KPLGRGAFGQVIEVAVKMLALMSELKILIHIGLNVVNLLGAMVIVEFCKFGNLSTYLRSFLASRKCIHRDLAARNILLICDFGL_ |
| Ligand affinity | |
| ChEMBL ID: | CHEMBL153843 |
| Bioaffinities: | 43 records for 8 kinases |
| Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
|---|---|---|---|---|---|---|
| Homo sapiens | Epidermal growth factor receptor erbB1 | 5 | 5 | 5 | pIC50 | 1 |
| Homo sapiens | Macrophage colony stimulating factor receptor | 6.4 | 6.4 | 6.4 | pIC50 | 1 |
| Homo sapiens | Platelet-derived growth factor receptor beta | 6.2 | 6.2 | 6.2 | pIC50 | 1 |
| Homo sapiens | Stem cell growth factor receptor | 6.6 | 6.6 | 6.6 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase ABL | 5.6 | 5.6 | 5.6 | pIC50 | 1 |
| Homo sapiens | Vascular endothelial growth factor receptor 1 | 6.8 | 6.8 | 7.5 | pIC50 | 11 |
| Homo sapiens | Vascular endothelial growth factor receptor 2 | 7.5 | 6.8 | 8.9 | pIC50 | 25 |
| Homo sapiens | Vascular endothelial growth factor receptor 3 | 7.8 | 7.8 | 7.8 | 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 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 1067 | 85 _ _ | |||||||||||||||
| •• | •• | ||||||||||||||||||
Interaction pattern search
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