5O2B - chain A (model B) | WNK lysine deficient protein kinase 3
Structure information
PDB: | 5O2B |
PubMed: | - |
Release date: | 2017-06-28 |
Resolution: | 2.04 Å |
Kinase: | WNK3 (Wnk3) |
Family: | WNK |
Group: | Other |
Species: | HUMAN |
Quality Score: | 8 |
Missing Residues: | 0 |
Missing Atoms: | 25 |
DFG conformation: | in |
αC-helix conformation: | out |
Salt bridge KIII.17 and EαC.24: | No |
ASP rotation (xDFG.81) : | 308° |
PHE rotation (xDFG.82) : | 359° |
Activation loop position: | -3.4Å |
αC-helix position: | 21Å |
G-rich loop angle: | 55.2° |
G-rich loop distance: | 15.7Å |
G-rich loop rotation: | 32.6° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond protein
I3
H-bond protein
I7
H-bond ligand
H-bond protein
Binding pocket sequence
Uniprot | IELGRGAFKTVYKVAWCELRFKEEAEMLKGLQPNIVRFYDSVLVTELMTSGTLKTYLKRHTRTPPIIHRDLKCDNIFIIGDLGLA |
Structure: | IELGRGAFKTVYKVAWCELRFKEEAEMLKGLQPNIVRFYDSVLVTELMTSGTLKTYLKRHTRTPPIIHRDLKCDNIFIIGDLGLA |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: KS1
Ligand Name: 1-cyclopentyl-3-(1H-pyrrolo[2,3-b]pyridin-5-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
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- 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 I 151 | 2 E 152 | 3 L 153 | 4 G 154 | 5 R 155 | 6 G 156 | 7 A 157 | 8 F 158 | 9 K 159 | 10 T 160 | 11 V 161 | 12 Y 162 | 13 K 163 | 14 V 173 | 15 A 174 | 16 W 175 | 17 C 176 | 18 E 177 | 19 L 178 | 20 R 190 |
■ | ■ | ■▲ | ■ | ■ | ■ | ||||||||||||||
αC | b.l | IV | |||||||||||||||||
21 F 191 | 22 K 192 | 23 E 193 | 24 E 194 | 25 A 195 | 26 E 196 | 27 M 197 | 28 L 198 | 29 K 199 | 30 G 200 | 31 L 201 | 32 Q 202 | 33 P 204 | 34 N 205 | 35 I 206 | 36 V 207 | 37 R 208 | 38 F 209 | 39 Y 210 | 40 D 211 |
■ | |||||||||||||||||||
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 S 212 | 42 V 224 | 43 L 225 | 44 V 226 | 45 T 227 | 46 E 228 | 47 L 229 | 48 M 230 | 49 T 231 | 50 S 232 | 51 G 233 | 52 T 234 | 53 L 235 | 54 K 236 | 55 T 237 | 56 Y 238 | 57 L 239 | 58 K 240 | 59 R 241 | 60 H 265 |
■ | ■ | ▲ | ■ | ■▲ | ■ | ||||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 T 266 | 62 R 267 | 63 T 268 | 64 P 269 | 65 P 270 | 66 I 271 | 67 I 272 | 68 H 273 | 69 R 274 | 70 D 275 | 71 L 276 | 72 K 277 | 73 C 278 | 74 D 279 | 75 N 280 | 76 I 281 | 77 F 282 | 78 I 283 | 79 I 292 | 80 G 293 |
■♦ | |||||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 294 | 82 L 295 | 83 G 296 | 84 L 297 | 85 A 298 | |||||||||||||||
■▲ | ■ |
Binding affinities
ChEMBL ID:CHEMBL1081312Bioaffinities: 76 records for 59 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | Activin receptor type-1 | 7.2 | 7.2 | 7.2 | pKi | 1 |
Homo sapiens | ALK tyrosine kinase receptor | 6.2 | 6.2 | 6.2 | pKi | 1 |
Homo sapiens | AMP-activated protein kinase, alpha-1 subunit | 5.6 | 5.6 | 5.6 | pKi | 1 |
Homo sapiens | cAMP-dependent protein kinase alpha-catalytic subunit | 6.1 | 6.1 | 6.1 | pKi | 1 |
Homo sapiens | Casein kinase I alpha | 7.4 | 7.4 | 7.4 | pKi | 1 |
Homo sapiens | Cell division protein kinase 8 | 5.9 | 5.9 | 5.9 | pKi | 1 |
Homo sapiens | c-Jun N-terminal kinase 1 | 5.6 | 5.6 | 5.6 | pKi | 1 |
Homo sapiens | c-Jun N-terminal kinase 2 | 5.9 | 5.9 | 5.9 | pKi | 1 |
Homo sapiens | Cyclin-dependent kinase 5 | 5.9 | 5.9 | 5.9 | pKi | 1 |
Homo sapiens | Death-associated protein kinase 3 | 5.3 | 5.3 | 5.3 | pKi | 1 |
Homo sapiens | DNA-dependent protein kinase | 7.2 | 7.2 | 7.2 | pIC50 | 1 |
Homo sapiens | Dual specificity mitogen-activated protein kinase kinase 1 | 6.4 | 6.4 | 6.4 | pKi | 1 |
Homo sapiens | Dual specificity mitogen-activated protein kinase kinase 2 | 6 | 6 | 6 | pKi | 1 |
Homo sapiens | Dual specificity protein kinase CLK2 | 6 | 6 | 6 | pKi | 1 |
Homo sapiens | Dual specificity protein kinase CLK4 | 6.1 | 6.1 | 6.1 | pKi | 1 |
Homo sapiens | Ephrin type-B receptor 4 | 6.7 | 6.7 | 6.7 | pIC50 | 1 |
Homo sapiens | Epidermal growth factor receptor erbB1 | 6.6 | 6.6 | 6.6 | pIC50 | 2 |
Homo sapiens | Fibroblast growth factor receptor 1 | 7 | 7 | 7 | pKi | 1 |
Homo sapiens | Focal adhesion kinase 1 | 5.9 | 5.9 | 5.9 | pKi | 1 |
Homo sapiens | Glycogen synthase kinase-3 alpha | 5.7 | 5.7 | 5.7 | pKi | 1 |
Homo sapiens | Inhibitor of nuclear factor kappa B kinase epsilon subunit | 5.8 | 5.8 | 5.8 | pKi | 1 |
Homo sapiens | Insulin-like growth factor I receptor | 6.4 | 6.4 | 6.4 | pKi | 1 |
Homo sapiens | Leucine-rich repeat serine/threonine-protein kinase 2 | 7.2 | 7.2 | 7.2 | pKi | 1 |
Homo sapiens | Leukocyte tyrosine kinase receptor | 6.8 | 6.8 | 6.8 | pKi | 1 |
Homo sapiens | LIM domain kinase 1 | 6.8 | 6.8 | 6.8 | pKi | 1 |
Homo sapiens | Macrophage colony stimulating factor receptor | 6.4 | 6.4 | 6.4 | pKi | 1 |
Homo sapiens | Macrophage-stimulating protein receptor | 6.9 | 6.9 | 6.9 | pKi | 1 |
Homo sapiens | MAP kinase p38 alpha | 5.6 | 5.6 | 5.6 | pKi | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 2 | 6.5 | 6.5 | 6.5 | pKi | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 4 | 6.2 | 6.2 | 6.2 | pKi | 1 |
Homo sapiens | Mitogen-activated protein kinase kinase kinase kinase 5 | 5.9 | 5.9 | 5.9 | pKi | 1 |
Homo sapiens | PI3-kinase p110-alpha subunit | 7.3 | 7.3 | 7.3 | pIC50 | 3 |
Homo sapiens | PI3-kinase p110-beta subunit | 5.9 | 5.9 | 5.9 | pIC50 | 2 |
Homo sapiens | PI3-kinase p110-delta subunit | 6.8 | 6.8 | 6.8 | pIC50 | 2 |
Homo sapiens | PI3-kinase p110-gamma subunit | 6 | 6 | 6 | pIC50 | 2 |
Homo sapiens | PI4-kinase beta subunit | 7.2 | 7.2 | 7.2 | pIC50 | 1 |
Homo sapiens | Platelet-derived growth factor receptor alpha | 6.5 | 6.5 | 6.5 | pKi | 1 |
Homo sapiens | Platelet-derived growth factor receptor beta | 6.4 | 6.4 | 6.4 | pKi | 1 |
Homo sapiens | Protein kinase C nu | 6.6 | 6.6 | 6.6 | pKi | 1 |
Homo sapiens | Protein kinase C theta | 6.3 | 6.3 | 6.3 | pKi | 1 |
Homo sapiens | Rho-associated protein kinase 1 | 6.7 | 6.7 | 6.7 | pKi | 1 |
Homo sapiens | Rho-associated protein kinase 2 | 7.4 | 7.4 | 7.4 | pKi | 1 |
Homo sapiens | Serine-protein kinase ATR | 5.9 | 5.9 | 5.9 | pIC50 | 1 |
Homo sapiens | Serine/threonine-protein kinase c-TAK1 | 6.1 | 6.1 | 6.1 | pKi | 1 |
Homo sapiens | Serine/threonine-protein kinase mTOR | 8 | 8 | 8 | pIC50 | 2 |
Homo sapiens | Serine/threonine-protein kinase PAK 4 | 6.2 | 6.2 | 6.2 | pKi | 1 |
Homo sapiens | Serine/threonine-protein kinase TAO1 | 5.6 | 5.6 | 5.6 | pKi | 1 |
Homo sapiens | Tyrosine kinase non-receptor protein 2 | 6.4 | 6.4 | 6.4 | pKi | 1 |
Homo sapiens | Tyrosine-protein kinase ABL | 7.8 | 7.8 | 8.7 | pIC50 | 3 |
Homo sapiens | Tyrosine-protein kinase ABL | 7.8 | 7.8 | 7.8 | pKi | 1 |
Homo sapiens | Tyrosine-protein kinase BTK | 5.8 | 5.8 | 5.8 | pKi | 1 |
Homo sapiens | Tyrosine-protein kinase FYN | 7.1 | 7.1 | 7.1 | pKi | 1 |
Homo sapiens | Tyrosine-protein kinase HCK | 8.1 | 8.1 | 8.1 | pIC50 | 2 |
Homo sapiens | Tyrosine-protein kinase JAK2 | 6 | 6 | 6 | pKi | 2 |
Homo sapiens | Tyrosine-protein kinase LCK | 6.8 | 6.8 | 6.8 | pKi | 1 |
Homo sapiens | Tyrosine-protein kinase receptor RET | 8.9 | 8.9 | 8.9 | pKi | 1 |
Homo sapiens | Tyrosine-protein kinase receptor TYRO3 | 6.1 | 6.1 | 6.1 | pKi | 1 |
Homo sapiens | Tyrosine-protein kinase SRC | 7.9 | 7.9 | 7.9 | pIC50 | 3 |
Homo sapiens | Vascular endothelial growth factor receptor 1 | 7.2 | 7.2 | 7.2 | pKi | 1 |
Homo sapiens | Vascular endothelial growth factor receptor 2 | 7.9 | 7.4 | 7.9 | pIC50 | 3 |
Homo sapiens | Vascular endothelial growth factor receptor 2 | 8.3 | 8.3 | 8.3 | pKi | 1 |