PDB-code
| Kinase structure | |
| Kinase: | CDK5 |
| Family: | CDK |
| Group: | CMGC |
| Species: | HUMAN |
| IUPHAR/BPS ID: | 1977 |
| PDB: | 7VDP |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2022-03-09 |
| PubMed: | 35143203 |
| Chain: | A |
| Orthosteric ligand: | 65L |
 | |
| Structural information | |
| DFG conformation: | in |
| αC-helix conformation: | in |
| G-rich loop angle (distance): | - |
| G-rich loop rotation: | - |
| Quality Score: | 6.8 |
| Resolution: | 2.09 Å |
| Missing Residues: | 3 |
| Missing Atoms: | 0 |
| Ligand binding mode | ||||
| Pockets | Subpockets | Waters | ||
| front | Cluster I10 | Ligand No | Protein Yes | |
| Pocket alignment | |
| Uniprot sequence: | EKIGEGTYGTVFKVALKRVSALREICLLKELKKNIVRLHDVTLVFEFCD-QDLKKYFDSFCHSRNVLHRDLKPQNLLILADFGLA |
| Sequence structure: | EKIGE___GTVFKVALKRVSALREICLLKELKKNIVRLHDVTLVFEFCD_QDLKKYFDSFCHSRNVLHRDLKPQNLLILADFGLA |
| 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 E 8 | 2 K 9 | 3 I 10 | 4 G 11 | 5 E 12 | 6 _ _ | 7 _ _ | 8 _ _ | 9 G 16 | 10 T 17 | 11 V 18 | 12 F 19 | 13 K 20 | 14 V 30 | 15 A 31 | 16 L 32 | 17 K 33 | 18 R 34 | 19 V 35 | 20 S 47 |
| • | • | • | • | ||||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 A 48 | 22 L 49 | 23 R 50 | 24 E 51 | 25 I 52 | 26 C 53 | 27 L 54 | 28 L 55 | 29 K 56 | 30 E 57 | 31 L 58 | 32 K 59 | 33 K 61 | 34 N 62 | 35 I 63 | 36 V 64 | 37 R 65 | 38 L 66 | 39 H 67 | 40 D 68 |
| • | |||||||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 V 69 | 42 T 77 | 43 L 78 | 44 V 79 | 45 F 80 | 46 E 81 | 47 F 82 | 48 C 83 | 49 D 84 | 50 _ _ | 51 Q 85 | 52 D 86 | 53 L 87 | 54 K 88 | 55 K 89 | 56 Y 90 | 57 F 91 | 58 D 92 | 59 S 93 | 60 F 116 |
| •• | • | • | ••• | • | • | • | • | ||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 C 117 | 62 H 118 | 63 S 119 | 64 R 120 | 65 N 121 | 66 V 122 | 67 L 123 | 68 H 124 | 69 R 125 | 70 D 126 | 71 L 127 | 72 K 128 | 73 P 129 | 74 Q 130 | 75 N 131 | 76 L 132 | 77 L 133 | 78 I 134 | 79 L 142 | 80 A 143 |
| • | • | • | • | ||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 144 | 82 F 145 | 83 G 146 | 84 L 147 | 85 A 148 | |||||||||||||||
| ••• | |||||||||||||||||||
Interaction pattern search
Search KLIFS for kinase-ligand complexes with similar interaction patterns:
