PDB-code
| Kinase structure | |
| Kinase: | PKMYT1 (MYT1) |
| Family: | WEE |
| Group: | Other |
| Species: | HUMAN |
| IUPHAR/BPS ID: | 2167 |
| PDB: | 5VD1 |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2017-08-23 |
| PubMed: | 28792760 |
| Chain: | A |
| (Alternate) Model: | A |
| Orthosteric ligand: | P48 |
 | |
| More entries for 5VD1 | |||||
| 5VD1 | Alternative model: | B | Chain: | A | |
| Structural information | |
| DFG conformation: | in |
| αC-helix conformation: | in |
| G-rich loop angle (distance): | 57.2° (17.7Å) |
| G-rich loop rotation: | 52.6° |
| Quality Score: | 8 |
| Resolution: | 1.7 Å |
| Missing Residues: | 0 |
| Missing Atoms: | 0 |
| Ligand binding mode | ||||
| Pockets | Subpockets | Waters | ||
| front | Cluster I2 I4 I5 I9 | Ligand No No No No | Protein No Yes Yes Yes | |
| Pocket alignment | |
| Uniprot sequence: | SRLGHGSYGEVFKYAVKRSRKLAEVGSHEKVGPCCVRLEQAYLQTELC-GPSLQQHCEAHLHSQGLVHLDVKPANIFLLGDFGLL |
| Sequence structure: | SRLGHGSYGEVFKYAVKRSRKLAEVGSHEKVGPCCVRLEQAYLQTELC_GPSLQQHCEAHLHSQGLVHLDVKPANIFLLGDFGLL |
| Ligand affinity | |
| ChEMBL ID: | CHEMBL564829 |
| Bioaffinities: | 17 records for 15 kinases |
| Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
|---|---|---|---|---|---|---|
| Homo sapiens | Cyclin-dependent kinase 2 | 7.4 | 6.4 | 7.4 | pIC50 | 3 |
| Homo sapiens | Epidermal growth factor receptor erbB1 | 5.5 | 5.5 | 5.5 | pIC50 | 1 |
| Homo sapiens | Fibroblast growth factor receptor 1 | 5.9 | 5.9 | 5.9 | pIC50 | 1 |
| Homo sapiens | Nerve growth factor receptor Trk-A | 7.3 | 7.3 | 7.3 | pIC50 | 1 |
| Homo sapiens | Serine/threonine-protein kinase Aurora-A | 6 | 6 | 6 | pIC50 | 1 |
| Homo sapiens | Serine/threonine-protein kinase Aurora-B | 5.4 | 5.4 | 5.4 | pIC50 | 1 |
| Homo sapiens | Serine/threonine-protein kinase NEK6 | 6 | 6 | 6 | pIC50 | 1 |
| Homo sapiens | Serine/threonine-protein kinase WEE1 | 7.9 | 7.9 | 7.9 | pKd | 1 |
| Homo sapiens | Stem cell growth factor receptor | 6.2 | 6.2 | 6.2 | pIC50 | 1 |
| Homo sapiens | Tyrosine- and threonine-specific cdc2-inhibitory kinase | 6 | 6 | 6 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase ABL | 6.3 | 6.3 | 6.3 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase LCK | 6.7 | 6.7 | 6.7 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase receptor RET | 5.7 | 5.7 | 5.7 | pIC50 | 1 |
| Homo sapiens | Vascular endothelial growth factor receptor 3 | 6 | 6 | 6 | pIC50 | 1 |
| Homo sapiens | Wee1-like protein kinase 2 | 7.6 | 7.6 | 7.6 | 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 S 114 | 2 R 115 | 3 L 116 | 4 G 117 | 5 H 118 | 6 G 119 | 7 S 120 | 8 Y 121 | 9 G 122 | 10 E 123 | 11 V 124 | 12 F 125 | 13 K 126 | 14 Y 136 | 15 A 137 | 16 V 138 | 17 K 139 | 18 R 140 | 19 S 141 | 20 R 153 |
| • | • | • | • | • | •• | ||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 K 154 | 22 L 155 | 23 A 156 | 24 E 157 | 25 V 158 | 26 G 159 | 27 S 160 | 28 H 161 | 29 E 162 | 30 K 163 | 31 V 164 | 32 G 165 | 33 P 168 | 34 C 169 | 35 C 170 | 36 V 171 | 37 R 172 | 38 L 173 | 39 E 174 | 40 Q 175 |
| • | |||||||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 A 176 | 42 Y 184 | 43 L 185 | 44 Q 186 | 45 T 187 | 46 E 188 | 47 L 189 | 48 C 190 | 49 _ _ | 50 G 191 | 51 P 192 | 52 S 193 | 53 L 194 | 54 Q 195 | 55 Q 196 | 56 H 197 | 57 C 198 | 58 E 199 | 59 A 200 | 60 H 223 |
| • | • | ••• | • | • | • | ||||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 L 224 | 62 H 225 | 63 S 226 | 64 Q 227 | 65 G 228 | 66 L 229 | 67 V 230 | 68 H 231 | 69 L 232 | 70 D 233 | 71 V 234 | 72 K 235 | 73 P 236 | 74 A 237 | 75 N 238 | 76 I 239 | 77 F 240 | 78 L 241 | 79 L 249 | 80 G 250 |
| •• | • | ||||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 251 | 82 F 252 | 83 G 253 | 84 L 254 | 85 L 255 | |||||||||||||||
| • | |||||||||||||||||||
Interaction pattern search
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