PDB-code
| Kinase structure | |
| Kinase: | PDPK1 (PDK1) |
| Family: | PDK1 |
| Group: | AGC |
| Species: | HUMAN |
| IUPHAR/BPS ID: | 1519 |
| PDB: | 5LVN |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2016-10-19 |
| PubMed: | 27693059 |
| Chain: | A |
| (Alternate) Model: | A |
| Orthosteric ligand: | ADN |
 | |
| More entries for 5LVN | |||||
| 5LVN | Alternative model: | B | Chain: | A | |
| Structural information | |
| DFG conformation: | in |
| αC-helix conformation: | in |
| G-rich loop angle (distance): | 59.1° (17.3Å) |
| G-rich loop rotation: | 52.3° |
| Quality Score: | 8 |
| Resolution: | 1.38 Å |
| Missing Residues: | 0 |
| Missing Atoms: | 22 |
| Ligand binding mode | ||||
| Pockets | Subpockets | Waters | ||
| front | Cluster I1 I3 I4 I6 I7 | Ligand Yes Yes No Yes Yes | Protein Yes Yes Yes Yes No | |
| Allosteric Ligand | |||||||||||||||||||
| Allosteric ligand: | DTD | ||||||||||||||||||
 | |||||||||||||||||||
| Pocket alignment | |
| Uniprot sequence: | KILGEGSFSTVVLYAIKILYVTRERDVMSRLDPFFVKLYFTYFGLSYAKNGELLKYIRKYLHGKGIIHRDLKPENILLITDFGTA |
| Sequence structure: | KILGEGSFSTVVLYAIKILYVTRERDVMSRLDPFFVKLYFTYFGLSYAKNGELLKYIRKYLHGKGIIHRDLKPENILLITDFGTA |
| Ligand affinity | |
| ChEMBL ID: | CHEMBL477 |
| Bioaffinities: | 2 records for 1 kinase |
| Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
|---|---|---|---|---|---|---|
| Homo sapiens | Mitogen-activated protein kinase kinase kinase 7 | 4.5 | 4.5 | 5.4 | pKd | 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 86 | 2 I 87 | 3 L 88 | 4 G 89 | 5 E 90 | 6 G 91 | 7 S 92 | 8 F 93 | 9 S 94 | 10 T 95 | 11 V 96 | 12 V 97 | 13 L 98 | 14 Y 108 | 15 A 109 | 16 I 110 | 17 K 111 | 18 I 112 | 19 L 113 | 20 Y 126 |
| • | • | • | • | • | |||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 V 127 | 22 T 128 | 23 R 129 | 24 E 130 | 25 R 131 | 26 D 132 | 27 V 133 | 28 M 134 | 29 S 135 | 30 R 136 | 31 L 137 | 32 D 138 | 33 P 140 | 34 F 141 | 35 F 142 | 36 V 143 | 37 K 144 | 38 L 145 | 39 Y 146 | 40 F 147 |
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 T 148 | 42 Y 156 | 43 F 157 | 44 G 158 | 45 L 159 | 46 S 160 | 47 Y 161 | 48 A 162 | 49 K 163 | 50 N 164 | 51 G 165 | 52 E 166 | 53 L 167 | 54 L 168 | 55 K 169 | 56 Y 170 | 57 I 171 | 58 R 172 | 59 K 173 | 60 Y 195 |
| • | •• | •• | •• | ||||||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 L 196 | 62 H 197 | 63 G 198 | 64 K 199 | 65 G 200 | 66 I 201 | 67 I 202 | 68 H 203 | 69 R 204 | 70 D 205 | 71 L 206 | 72 K 207 | 73 P 208 | 74 E 209 | 75 N 210 | 76 I 211 | 77 L 212 | 78 L 213 | 79 I 221 | 80 T 222 |
| • | |||||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 223 | 82 F 224 | 83 G 225 | 84 T 226 | 85 A 227 | |||||||||||||||
Interaction pattern search
Search KLIFS for kinase-ligand complexes with similar interaction patterns:
