5UUU - chain A (model B) | Adrenergic, beta, receptor kinase 1
Structure information
PDB: | 5UUU |
PubMed: | 28699740 |
Release date: | 2017-07-26 |
Resolution: | 2.7 Å |
Kinase: | GRK2 (BARK1) |
Family: | GRK |
Group: | AGC |
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 (3Å) |
ASP rotation (xDFG.81) : | 350° |
PHE rotation (xDFG.82) : | 351° |
Activation loop position: | -3.9Å |
αC-helix position: | 18.4Å |
G-rich loop angle: | 61.3° |
G-rich loop distance: | 18.2Å |
G-rich loop rotation: | 68.5° |
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
I5
H-bond protein
I6
H-bond ligand
H-bond protein
Binding pocket sequence
Uniprot | RIIGRGGFGEVYGYAMKCLLALNERIMLSLVSPFIVCMSYASFILDLMNGGDLHYHLSQHMHNRFVVYRDLKPANILLISDLGLA |
Structure: | RIIGRGGFGEVYGYAMKCLLALNERIMLSLVSPFIVCMSYASFILDLMNGGDLHYHLSQHMHNRFVVYRDLKPANILLISDLGLA |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: QRW
Ligand Name: 3-({[4-methyl-5-(pyridin-4-yl)-4H-1,2,4-triazol-3-yl]methyl}amino)-N-[2-(trifluoromethyl)benzyl]benzamide
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- LABELS
- KLIFS residue #
- Amino Acid
- None
- COLORS
- Interaction types
- KLIFS (all res.)
- KLIFS (interacting res.)
- None
- OTHER
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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 R 195 | 2 I 196 | 3 I 197 | 4 G 198 | 5 R 199 | 6 G 200 | 7 G 201 | 8 F 202 | 9 G 203 | 10 E 204 | 11 V 205 | 12 Y 206 | 13 G 207 | 14 Y 217 | 15 A 218 | 16 M 219 | 17 K 220 | 18 C 221 | 19 L 222 | 20 L 235 |
■ | ■ | ■ | ■ | ■♦▲ | ■ | ■ | ■ | ■ | ■▲ | ■ | ■ | ||||||||
αC | b.l | IV | |||||||||||||||||
21 A 236 | 22 L 237 | 23 N 238 | 24 E 239 | 25 R 240 | 26 I 241 | 27 M 242 | 28 L 243 | 29 S 244 | 30 L 245 | 31 V 246 | 32 S 247 | 33 P 252 | 34 F 253 | 35 I 254 | 36 V 255 | 37 C 256 | 38 M 257 | 39 S 258 | 40 Y 259 |
■ | |||||||||||||||||||
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 A 260 | 42 S 268 | 43 F 269 | 44 I 270 | 45 L 271 | 46 D 272 | 47 L 273 | 48 M 274 | 49 N 275 | 50 G 276 | 51 G 277 | 52 D 278 | 53 L 279 | 54 H 280 | 55 Y 281 | 56 H 282 | 57 L 283 | 58 S 284 | 59 Q 285 | 60 H 307 |
■ | ■ | ■▲ | |||||||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 M 308 | 62 H 309 | 63 N 310 | 64 R 311 | 65 F 312 | 66 V 313 | 67 V 314 | 68 Y 315 | 69 R 316 | 70 D 317 | 71 L 318 | 72 K 319 | 73 P 320 | 74 A 321 | 75 N 322 | 76 I 323 | 77 L 324 | 78 L 325 | 79 I 333 | 80 S 334 |
■ | |||||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 335 | 82 L 336 | 83 G 337 | 84 L 338 | 85 A 339 | |||||||||||||||
▲ | ■ | ■ |
Binding affinities
ChEMBL ID:CHEMBL1738877Bioaffinities: 13 records for 10 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Bos taurus | Beta-adrenergic receptor kinase 1 | 6.5 | 6.5 | 7.5 | pIC50 | 2 |
Homo sapiens | Beta-adrenergic receptor kinase 2 | 8.3 | 8.3 | 8.3 | pIC50 | 1 |
Homo sapiens | G-protein coupled receptor kinase 2 | 5 | 5 | 5 | pEC50 | 1 |
Homo sapiens | G-protein coupled receptor kinase 2 | 7.5 | 7.5 | 7.8 | pIC50 | 2 |
Bos taurus | G protein-coupled receptor kinase 5 | 5 | 5 | 5 | pIC50 | 1 |
Homo sapiens | G protein-coupled receptor kinase 5 | 5.6 | 5.6 | 5.6 | pIC50 | 1 |
Homo sapiens | G protein-coupled receptor kinase 7 | 4.6 | 4.6 | 4.6 | pIC50 | 1 |
Homo sapiens | Protein kinase C alpha | 5.1 | 5.1 | 5.1 | pIC50 | 1 |
Homo sapiens | Rho-associated protein kinase 2 | 5.9 | 5.9 | 5.9 | pIC50 | 1 |
Bos taurus | Rhodopsin kinase | 4.3 | 4.3 | 4.3 | pIC50 | 1 |
Homo sapiens | Rhodopsin kinase | 5.5 | 5.5 | 5.5 | pIC50 | 1 |