PDB-code
| Kinase structure | |
| Kinase: | KDR |
| Family: | VEGFR |
| Group: | TK |
| Species: | HUMAN |
| IUPHAR/BPS ID: | 1813 |
| PDB: | 4AGC |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2012-09-26 |
| PubMed: | 22988103 |
| Chain: | A |
| Orthosteric ligand: | AXI |
 | |
| Structural information | |
| DFG conformation: | out |
| αC-helix conformation: | in |
| G-rich loop angle (distance): | 59.3° (18.3Å) |
| G-rich loop rotation: | 43.6° |
| Quality Score: | 7.6 |
| Resolution: | 2 Å |
| Missing Residues: | 0 |
| Missing Atoms: | 0 |
| Ligand binding mode | ||||
| Pockets | Subpockets | Waters | ||
| front gate back | BP-I-B | Cluster I1 I9 | Ligand No Yes | Protein Yes Yes |
| Pocket alignment | |
| Uniprot sequence: | KPLGRGAFGQVIEVAVKMLALMSELKILIHIGLNVVNLLGAMVIVEFCKFGNLSTYLRSFLASRKCIHRDLAARNILLICDFGLA |
| Sequence structure: | KPLGRGAFGQVIEVAVKMLALMSELKILIHIGLNVVNLLGAMVIVEFCKFGNLSTYLRSFLASRKCIHRDLAARNILLICDFGLA |
| Ligand affinity | |
| ChEMBL ID: | CHEMBL1289926 |
| Bioaffinities: | 153 records for 98 kinases |
| Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
|---|---|---|---|---|---|---|
| Homo sapiens | Activin receptor type-2B | 5.3 | 5.3 | 5.3 | pKd | 1 |
| Homo sapiens | Adaptor-associated kinase | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Ankyrin repeat and protein kinase domain-containing protein 1 | 5.4 | 5.4 | 5.4 | pKd | 1 |
| Homo sapiens | BMP-2-inducible protein kinase | 6 | 6 | 6 | pKd | 1 |
| Homo sapiens | Bone morphogenetic protein receptor type-1B | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | CaM-kinase kinase alpha | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | CaM-kinase kinase beta | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | Casein kinase II alpha (prime) | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | c-Jun N-terminal kinase 1 | 5.4 | 5.4 | 5.4 | pKd | 1 |
| Homo sapiens | c-Jun N-terminal kinase 3 | 6 | 6 | 6 | pKd | 1 |
| Homo sapiens | Cyclin-dependent kinase-like 2 | 6.3 | 6.3 | 6.3 | pKd | 1 |
| Homo sapiens | Discoidin domain-containing receptor 2 | 5.3 | 5.3 | 5.3 | pKd | 1 |
| Homo sapiens | Dual specificity mitogen-activated protein kinase kinase 1 | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Dual specificity mitogen-activated protein kinase kinase 2 | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Dual specificity mitogen-activated protein kinase kinase 5 | 6.9 | 6.9 | 6.9 | pKd | 1 |
| Homo sapiens | Dual specificity protein kinase TTK | 5.4 | 5.4 | 5.4 | pKd | 1 |
| Homo sapiens | Dual specificity testis-specific protein kinase 1 | 5.4 | 5.4 | 5.4 | pKd | 1 |
| Homo sapiens | Epidermal growth factor receptor erbB1 | 5.2 | 5.2 | 5.6 | pKd | 2 |
| Homo sapiens | Epithelial discoidin domain-containing receptor 1 | 6.5 | 6.5 | 6.5 | pKd | 1 |
| Homo sapiens | Fibroblast growth factor receptor 1 | 6.4 | 6.4 | 6.4 | pKd | 1 |
| Homo sapiens | Fibroblast growth factor receptor 1 | 7.3 | 7.3 | 7.3 | pKi | 1 |
| Homo sapiens | Fibroblast growth factor receptor 2 | 7 | 7 | 7 | pKd | 1 |
| Homo sapiens | Fibroblast growth factor receptor 3 | 6.7 | 6.7 | 6.7 | pKd | 2 |
| Homo sapiens | G protein-coupled receptor kinase 4 | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Hepatocyte growth factor receptor | 6 | 6 | 6.1 | pKd | 3 |
| Homo sapiens | Hormonally up-regulated neu tumor-associated kinase | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | Interferon-induced, double-stranded RNA-activated protein kinase | 5.1 | 5.1 | 5.1 | pKd | 1 |
| Homo sapiens | Interleukin-1 receptor-associated kinase 1 | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | Leucine-rich repeat serine/threonine-protein kinase 2 | 6 | 6 | 6 | pKd | 2 |
| Homo sapiens | Macrophage colony stimulating factor receptor | 7.7 | 7.7 | 7.7 | pKd | 1 |
| Homo sapiens | Misshapen-like kinase 1 | 6.3 | 6.3 | 6.3 | pKd | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase 12 | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase 3 | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase 4 | 5.3 | 5.3 | 5.3 | pKd | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase 9 | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 1 | 6.5 | 6.5 | 6.5 | pKd | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 2 | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 3 | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 4 | 6.5 | 6.5 | 6.5 | pKd | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 5 | 6.3 | 6.3 | 6.3 | pKd | 1 |
| Homo sapiens | Mixed lineage kinase 7 | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Myosin IIIA | 5.7 | 5.7 | 5.7 | pKd | 1 |
| Homo sapiens | Myosin light chain kinase | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | myosin light chain kinase 2 | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Nerve growth factor receptor Trk-A | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | Non-receptor tyrosine-protein kinase TNK1 | 6.8 | 6.8 | 6.8 | pKd | 1 |
| Homo sapiens | NUAK family SNF1-like kinase 2 | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Platelet-derived growth factor receptor alpha | 9.3 | 9.3 | 9.3 | pKd | 1 |
| Homo sapiens | Platelet-derived growth factor receptor beta | 9.2 | 9.2 | 9.2 | pKd | 1 |
| Homo sapiens | Protein kinase N2 | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Proto-oncogene tyrosine-protein kinase MER | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | Proto-oncogene tyrosine-protein kinase ROS | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | Receptor-interacting serine/threonine-protein kinase 1 | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Receptor-interacting serine/threonine-protein kinase 4 | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase 10 | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase 16 | 6.4 | 6.4 | 6.4 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase 2 | 6 | 6 | 6 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase Aurora-A | 7.1 | 7.1 | 7.1 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase Aurora-B | 8 | 8 | 8 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase Aurora-C | 8.9 | 8.9 | 8.9 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase GAK | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase MRCK beta | 5.3 | 5.3 | 5.3 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase MST1 | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase MST2 | 5.7 | 5.7 | 5.7 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase PAK 4 | 5.4 | 5.4 | 5.4 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase PCTAIRE-1 | 5.3 | 5.3 | 5.3 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase PLK4 | 7.3 | 7.3 | 7.4 | pIC50 | 3 |
| Homo sapiens | Serine/threonine-protein kinase PLK4 | 7.8 | 7.8 | 7.8 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase PLK4 | 8.4 | 8.4 | 8.4 | pKi | 3 |
| Homo sapiens | Serine/threonine-protein kinase RIO1 | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase RIO3 | 6 | 6 | 6 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase RIPK2 | 5 | 5 | 5 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase SIK1 | 5.7 | 5.7 | 5.7 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase SRPK1 | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase SRPK3 | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase ULK2 | 5 | 5 | 5 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase ULK3 | 6.2 | 6.2 | 6.2 | pKd | 1 |
| Homo sapiens | SPS1/STE20-related protein kinase YSK4 | 6.6 | 6.6 | 6.6 | pKd | 1 |
| Homo sapiens | Stem cell growth factor receptor | 8.5 | 5.4 | 9.3 | pKd | 8 |
| Homo sapiens | TRAF2- and NCK-interacting kinase | 6.8 | 6.8 | 6.8 | pKd | 1 |
| Homo sapiens | Tyrosine kinase non-receptor protein 2 | 5.2 | 5.2 | 5.2 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase ABL | 8.6 | 8.1 | 9.4 | pIC50 | 4 |
| Homo sapiens | Tyrosine-protein kinase ABL | 7.1 | 5.6 | 8.8 | pKd | 15 |
| Homo sapiens | Tyrosine-protein kinase ABL2 | 7.2 | 7.2 | 7.2 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase BLK | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase CSK | 6 | 6 | 6 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase FGR | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase ITK/TSK | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase JAK2 | 5.5 | 5.5 | 5.5 | pKd | 2 |
| Homo sapiens | Tyrosine-protein kinase JAK3 | 5.5 | 5.5 | 5.5 | pKd | 2 |
| Homo sapiens | Tyrosine-protein kinase LCK | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase receptor FLT3 | 6.6 | 5.6 | 7.5 | pKd | 7 |
| Homo sapiens | Tyrosine-protein kinase receptor RET | 5.9 | 5.8 | 7 | pKd | 4 |
| Homo sapiens | Tyrosine-protein kinase receptor Tie-1 | 7 | 7 | 7 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase receptor UFO | 6.4 | 6.4 | 6.4 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase TIE-2 | 6.5 | 6.5 | 6.5 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase TXK | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase TYK2 | 5.4 | 5.4 | 5.4 | pKd | 2 |
| Homo sapiens | Tyrosine-protein kinase YES | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Vascular endothelial growth factor receptor 1 | 10 | 10 | 10 | pIC50 | 1 |
| Homo sapiens | Vascular endothelial growth factor receptor 1 | 8.2 | 8.2 | 8.2 | pKd | 1 |
| Homo sapiens | Vascular endothelial growth factor receptor 2 | 9.7 | 9.6 | 10 | pIC50 | 3 |
| Homo sapiens | Vascular endothelial growth factor receptor 2 | 8.2 | 8.2 | 8.2 | pKd | 1 |
| Homo sapiens | Vascular endothelial growth factor receptor 2 | 8.4 | 8.4 | 8.4 | pKi | 1 |
| Homo sapiens | Vascular endothelial growth factor receptor 3 | 10 | 10 | 10 | pIC50 | 1 |
| Homo sapiens | Vascular endothelial growth factor receptor 3 | 6.8 | 6.8 | 6.8 | pKd | 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
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