5VD1 - chain A (model B) | Protein kinase, membrane associated tyrosine/threonine 1
Structure information
| PDB: | 5VD1 |
| PubMed: | 28792760 |
| Release date: | 2017-08-23 |
| Resolution: | 1.7 Å |
| Kinase: | PKMYT1 (MYT1) |
| Family: | WEE |
| Group: | Other |
| Species: | HUMAN |
| Quality Score: | 8 |
| Missing Residues: | 0 |
| Missing Atoms: | 0 |
| DFG conformation: | in |
| αC-helix conformation: | in |
| Salt bridge KIII.17 and EαC.24: | Yes (2.7Å) |
| ASP rotation (xDFG.81) : | 336° |
| PHE rotation (xDFG.82) : | 354° |
| Activation loop position: | -3.1Å |
| αC-helix position: | 18.2Å |
| G-rich loop angle: | 57.2° |
| G-rich loop distance: | 17.7Å |
| G-rich loop rotation: | 52.6° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I2
No H-bonds
I4
H-bond protein
I5
H-bond protein
I9
H-bond protein
Binding pocket sequence
| Uniprot | SRLGHGSYGEVFKYAVKRSRKLAEVGSHEKVGPCCVRLEQAYLQTELC-GPSLQQHCEAHLHSQGLVHLDVKPANIFLLGDFGLL |
| Structure: | SRLGHGSYGEVFKYAVKRSRKLAEVGSHEKVGPCCVRLEQAYLQTELC_GPSLQQHCEAHLHSQGLVHLDVKPANIFLLGDFGLL |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: P48
Ligand Name: N,1,4,4-TETRAMETHYL-8-{[4-(4-METHYLPIPERAZIN-1-YL)PHENYL]AMINO}-4,5-DIHYDRO-1H-PYRAZOLO[4,3-H]QUINAZOLINE-3-CARBOXAMIDE
- Download image
- LABELS
- KLIFS residue #
- Amino Acid
- None
- COLORS
- Interaction types
- KLIFS (all res.)
- KLIFS (interacting res.)
- None
- OTHER
- Show/hide non-interacting res.
- En/disable resizing interacting res.
This ligand targets the following (sub)pockets:
| Main pockets | |
|---|---|
| Front | |
| Gate | |
| Back | |
| Subpockets | |
|---|---|
| FP-I | |
| FP-II | |
| BP-I-A | |
| BP-I-B | |
| BP-II-in | |
| BP-II-A-in | |
| BP-II-B-in | |
| BP-II-out | |
| BP-II-B | |
| BP-III | |
| BP-IV | |
| BP-V | |
Kinase-ligand interactions
■ 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 | |||||||||||||||
| ■ | |||||||||||||||||||
Binding affinities
ChEMBL ID:CHEMBL564829Bioaffinities: 98 records for 87 kinase(s)
| Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
|---|---|---|---|---|---|---|
| Homo sapiens | Activin receptor type-1 | 6.3 | 6.3 | 6.3 | pKd | 1 |
| Homo sapiens | Adaptor-associated kinase | 5.1 | 5.1 | 5.1 | pKd | 1 |
| Homo sapiens | Breakpoint cluster region protein | 6.2 | 6.2 | 6.2 | pKd | 2 |
| Homo sapiens | CaM-kinase kinase beta | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Casein kinase I alpha | 6 | 6 | 6 | pKd | 1 |
| Homo sapiens | Casein kinase I delta | 6.6 | 6.6 | 6.6 | pKd | 1 |
| Homo sapiens | Casein kinase I epsilon | 6.4 | 6.4 | 6.4 | pKd | 1 |
| Homo sapiens | Casein kinase II alpha (prime) | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | Chaperone activity of bc1 complex-like, mitochondrial | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | c-Jun N-terminal kinase 3 | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Cyclin-dependent kinase 2 | 7.4 | 6.4 | 7.4 | pIC50 | 3 |
| Homo sapiens | Cyclin-dependent kinase 2 | 6.1 | 6.1 | 6.1 | pKd | 1 |
| Homo sapiens | Cyclin-dependent kinase 4 | 5.4 | 5.4 | 5.4 | pKd | 1 |
| Homo sapiens | Cyclin-dependent kinase 5 | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Cyclin-dependent kinase 6 | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | Cyclin-dependent kinase 7 | 6.5 | 6.5 | 6.5 | pKd | 1 |
| Homo sapiens | Discoidin domain-containing receptor 2 | 5.4 | 5.4 | 5.4 | pKd | 1 |
| Homo sapiens | Dual specificity protein kinase CLK4 | 7.8 | 7.8 | 7.8 | pKd | 1 |
| Homo sapiens | Dual-specificity tyrosine-phosphorylation regulated kinase 1A | 7 | 7 | 7 | pKd | 1 |
| Homo sapiens | Dual specificty protein kinase CLK1 | 8.1 | 8.1 | 8.1 | pKd | 1 |
| Homo sapiens | Ephrin type-A receptor 2 | 6.2 | 6.2 | 6.2 | pKd | 1 |
| Homo sapiens | Ephrin type-A receptor 4 | 5.1 | 5.1 | 5.1 | pKd | 1 |
| Homo sapiens | Ephrin type-A receptor 5 | 6.8 | 6.8 | 6.8 | pKd | 1 |
| Homo sapiens | Ephrin type-B receptor 2 | 6.1 | 6.1 | 6.1 | pKd | 1 |
| Homo sapiens | Ephrin type-B receptor 3 | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Ephrin type-B receptor 4 | 6 | 6 | 6 | pKd | 1 |
| Homo sapiens | Epidermal growth factor receptor erbB1 | 5.5 | 5.5 | 5.5 | pIC50 | 1 |
| Homo sapiens | Epithelial discoidin domain-containing receptor 1 | 5.4 | 5.4 | 5.4 | pKd | 1 |
| Homo sapiens | Fibroblast growth factor receptor 1 | 5.9 | 5.9 | 5.9 | pIC50 | 1 |
| Homo sapiens | Fibroblast growth factor receptor 1 | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Inhibitor of nuclear factor kappa B kinase epsilon subunit | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | Interleukin-1 receptor-associated kinase 1 | 5.7 | 5.7 | 5.7 | pKd | 1 |
| Homo sapiens | Interleukin-1 receptor-associated kinase 3 | 6.5 | 6.5 | 6.5 | pKd | 1 |
| Homo sapiens | Interleukin-1 receptor-associated kinase 4 | 4.6 | 4.6 | 4.6 | pKd | 1 |
| Homo sapiens | Macrophage-stimulating protein receptor | 5.7 | 5.7 | 5.7 | pKd | 1 |
| Homo sapiens | MAP/microtubule affinity-regulating kinase 2 | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Maternal embryonic leucine zipper kinase | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase 11 | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase 4 | 5.4 | 5.4 | 5.4 | pKd | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 1 | 6.7 | 6.7 | 6.7 | pKd | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 2 | 4.9 | 4.9 | 4.9 | pKd | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 3 | 5.7 | 5.7 | 5.7 | pKd | 1 |
| Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 5 | 5 | 5 | 5 | pKd | 1 |
| Homo sapiens | Mitotic checkpoint serine/threonine-protein kinase BUB1 | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Myosin light chain kinase | 6.5 | 6.5 | 6.5 | pKd | 1 |
| Homo sapiens | Nerve growth factor receptor Trk-A | 7.3 | 7.3 | 7.3 | pIC50 | 1 |
| Homo sapiens | Nerve growth factor receptor Trk-A | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | Non-receptor tyrosine-protein kinase TNK1 | 5.3 | 5.3 | 5.3 | pKd | 1 |
| Homo sapiens | Phosphatidylinositol-5-phosphate 4-kinase type-2 gamma | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | Phosphorylase kinase gamma subunit 2 | 4.7 | 4.7 | 4.7 | pKd | 1 |
| Homo sapiens | Platelet-derived growth factor receptor beta | 6.3 | 6.3 | 6.3 | pKd | 1 |
| Homo sapiens | Protein kinase C nu | 6.9 | 6.9 | 6.9 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase 16 | 6 | 6 | 6 | pKd | 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 Aurora-B | 5.1 | 5.1 | 5.1 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase c-TAK1 | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase D2 | 6.8 | 6.8 | 6.8 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase GAK | 8.5 | 8.5 | 8.5 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase ICK | 6.1 | 6.1 | 6.1 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase LATS1 | 6.2 | 6.2 | 6.2 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase Nek3 | 5.6 | 5.6 | 5.6 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase NEK6 | 6 | 6 | 6 | pIC50 | 1 |
| Homo sapiens | Serine/threonine-protein kinase NEK9 | 4.7 | 4.7 | 4.7 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase PCTAIRE-1 | 6.3 | 6.3 | 6.3 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase PCTAIRE-2 | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase SIK2 | 7 | 7 | 7 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase SIK3 | 6.6 | 6.6 | 6.6 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase TAO1 | 6.5 | 6.5 | 6.5 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase TAO2 | 5.3 | 5.3 | 5.3 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase TAO3 | 5 | 5 | 5 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase TBK1 | 5.7 | 5.7 | 5.7 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase ULK1 | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | Serine/threonine-protein kinase WEE1 | 7.9 | 7.9 | 7.9 | pKd | 2 |
| Homo sapiens | Stem cell growth factor receptor | 6.2 | 6.2 | 6.2 | pIC50 | 1 |
| Homo sapiens | TRAF2- and NCK-interacting kinase | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Tyrosine- and threonine-specific cdc2-inhibitory kinase | 6 | 6 | 6 | pKd | 1 |
| Homo sapiens | Tyrosine kinase non-receptor protein 2 | 6.1 | 6.1 | 6.1 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase ABL | 6.3 | 6.3 | 6.3 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase ABL | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase ABL2 | 5.4 | 5.4 | 5.4 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase FRK | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase FYN | 5.8 | 5.8 | 5.8 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase HCK | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase LCK | 6.7 | 6.7 | 6.7 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase LCK | 6.2 | 6.2 | 6.2 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase Lyn | 5.5 | 5.5 | 5.5 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase receptor FLT3 | 7.3 | 7.3 | 7.3 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase receptor RET | 5.7 | 5.7 | 5.7 | pIC50 | 1 |
| Homo sapiens | Tyrosine-protein kinase receptor RET | 5.9 | 5.9 | 5.9 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase SRC | 5.3 | 5.3 | 5.3 | pKd | 1 |
| Homo sapiens | Tyrosine-protein kinase YES | 5.4 | 5.4 | 5.4 | pKd | 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 |