PDB-code
| Kinase structure | |
| Kinase: | VRK1 |
| Family: | VRK |
| Group: | CK1 |
| Species: | HUMAN |
| IUPHAR/BPS ID: | 2275 |
| PDB: | 6DD4 |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2018-05-23 |
| Chain: | B |
| (Alternate) Model: | B |
| Orthosteric ligand: | G6J |
 | |
| More entries for 6DD4 | |||||
| 6DD4 | Alternative model: | A | Chain: | A | |
| 6DD4 | Alternative model: | A | Chain: | B | |
| 6DD4 | Alternative model: | A | Chain: | C | |
| 6DD4 | Alternative model: | A | Chain: | D | |
| 6DD4 | Alternative model: | B | Chain: | A | |
| 6DD4 | Alternative model: | B | Chain: | C | |
| 6DD4 | Alternative model: | B | Chain: | D | |
| Structural information | |
| DFG conformation: | in |
| αC-helix conformation: | in |
| G-rich loop angle (distance): | - |
| G-rich loop rotation: | - |
| Quality Score: | 8.1 |
| Resolution: | 2.1 Å |
| Missing Residues: | 3 |
| Missing Atoms: | 7 |
| Ligand binding mode | ||||
| Pockets | Subpockets | Waters | ||
| front gate | BP-I-B | Cluster I5 | Ligand Yes | Protein Yes |
| Pocket alignment | |
| Uniprot sequence: | LPIGQGGFGCIYLCVVKVEPLFTELKFYQRAALGVPKYWGSFMIMDRFG-SDLQKIYEAYIHEHEYVHGDIKASNLLLLVDYGLA |
| Sequence structure: | LPIGQ___GCIYLCVVKVEPLFTELKFYQRAALGVPKYWGSFMIMDRFG_SDLQKIYEAYIHEHEYVHGDIKASNLLLLVDYGLA |
| 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 L 41 | 2 P 42 | 3 I 43 | 4 G 44 | 5 Q 45 | 6 _ _ | 7 _ _ | 8 _ _ | 9 G 49 | 10 C 50 | 11 I 51 | 12 Y 52 | 13 L 53 | 14 C 68 | 15 V 69 | 16 V 70 | 17 K 71 | 18 V 72 | 19 E 73 | 20 P 79 |
| • | • | • | • | • | •• | ||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 L 80 | 22 F 81 | 23 T 82 | 24 E 83 | 25 L 84 | 26 K 85 | 27 F 86 | 28 Y 87 | 29 Q 88 | 30 R 89 | 31 A 90 | 32 A 91 | 33 L 108 | 34 G 109 | 35 V 110 | 36 P 111 | 37 K 112 | 38 Y 113 | 39 W 114 | 40 G 115 |
| • | |||||||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 S 116 | 42 F 128 | 43 M 129 | 44 I 130 | 45 M 131 | 46 D 132 | 47 R 133 | 48 F 134 | 49 G 135 | 50 _ _ | 51 S 136 | 52 D 137 | 53 L 138 | 54 Q 139 | 55 K 140 | 56 I 141 | 57 Y 142 | 58 E 143 | 59 A 144 | 60 Y 167 |
| • | • | • | ••• | • | • | ||||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 I 168 | 62 H 169 | 63 E 170 | 64 H 171 | 65 E 172 | 66 Y 173 | 67 V 174 | 68 H 175 | 69 G 176 | 70 D 177 | 71 I 178 | 72 K 179 | 73 A 180 | 74 S 181 | 75 N 182 | 76 L 183 | 77 L 184 | 78 L 185 | 79 L 195 | 80 V 196 |
| • | • | ||||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 197 | 82 Y 198 | 83 G 199 | 84 L 200 | 85 A 201 | |||||||||||||||
| •• | |||||||||||||||||||
Interaction pattern search
Search KLIFS for kinase-ligand complexes with similar interaction patterns:
