6CZ3 - chain A (model A) | Protein tyrosine kinase 6
Structure information
PDB: | 6CZ3 |
PubMed: | 29879184 |
Release date: | 2018-06-20 |
Resolution: | 1.8 Å |
Kinase: | PTK6 (BRK) |
Family: | Src |
Group: | TK |
Species: | HUMAN |
Quality Score: | 8 |
Missing Residues: | 0 |
Missing Atoms: | 0 |
DFG conformation: | in |
αC-helix conformation: | out |
Salt bridge KIII.17 and EαC.24: | No (12.6Å) |
ASP rotation (xDFG.81) : | 318° |
PHE rotation (xDFG.82) : | 318° |
Activation loop position: | -4.9Å |
αC-helix position: | 21.1Å |
G-rich loop angle: | 49.1° |
G-rich loop distance: | 14.5Å |
G-rich loop rotation: | 67° |
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
I4
No H-bonds
I5
H-bond protein
Binding pocket sequence
Uniprot | RKLGSGYFGEVFEVAIKVIMLQSEIQAMKKLRKHILALYAVYIITELMAKGSLLELLRDYLESQNYIHRDLAARNILVVGDFGLA |
Structure: | RKLGSGYFGEVFEVAIKVIMLQSEIQAMKKLRKHILALYAVYIITELMAKGSLLELLRDYLESQNYIHRDLAARNILVVGDFGLA |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: FLJ
Ligand Name: (3-fluoro-4-{[6-methyl-3-(1H-pyrazol-4-yl)imidazo[1,2-a]pyrazin-8-yl]amino}phenyl)(morpholin-4-yl)methanone
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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 K 196 | 3 L 197 | 4 G 198 | 5 S 199 | 6 G 200 | 7 Y 201 | 8 F 202 | 9 G 203 | 10 E 204 | 11 V 205 | 12 F 206 | 13 E 207 | 14 V 216 | 15 A 217 | 16 I 218 | 17 K 219 | 18 V 220 | 19 I 221 | 20 M 231 |
■▲ | ■ | ■ | ■ | ■ | ■▲ | ||||||||||||||
αC | b.l | IV | |||||||||||||||||
21 L 232 | 22 Q 233 | 23 S 234 | 24 E 235 | 25 I 236 | 26 Q 237 | 27 A 238 | 28 M 239 | 29 K 240 | 30 K 241 | 31 L 242 | 32 R 243 | 33 K 245 | 34 H 246 | 35 I 247 | 36 L 248 | 37 A 249 | 38 L 250 | 39 Y 251 | 40 A 252 |
■ | |||||||||||||||||||
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 V 253 | 42 Y 261 | 43 I 262 | 44 I 263 | 45 T 264 | 46 E 265 | 47 L 266 | 48 M 267 | 49 A 268 | 50 K 269 | 51 G 270 | 52 S 271 | 53 L 272 | 54 L 273 | 55 E 274 | 56 L 275 | 57 L 276 | 58 R 277 | 59 D 278 | 60 Y 302 |
■ | ■ | ■▲▲ | ■ | ■ | ■ | ||||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 L 303 | 62 E 304 | 63 S 305 | 64 Q 306 | 65 N 307 | 66 Y 308 | 67 I 309 | 68 H 310 | 69 R 311 | 70 D 312 | 71 L 313 | 72 A 314 | 73 A 315 | 74 R 316 | 75 N 317 | 76 I 318 | 77 L 319 | 78 V 320 | 79 V 328 | 80 G 329 |
■ | |||||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 330 | 82 F 331 | 83 G 332 | 84 L 333 | 85 A 334 | |||||||||||||||
▲ |
Binding affinities
ChEMBL ID:CHEMBL1836855Bioaffinities: 1 record for 1 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | Tyrosine-protein kinase BRK | 7.2 | 7.2 | 7.2 | pIC50 | 1 |