5QIN - chain A (model B) | Transforming growth factor beta receptor II
Structure information
PDB: | 5QIN |
PubMed: | 30429955 |
Release date: | 2018-10-31 |
Resolution: | 1.57 Å |
Kinase: | TGFBR2 (TGFbR2) |
Family: | STKR |
Group: | TKL |
Species: | HUMAN |
Quality Score: | 9.4 |
Missing Residues: | 0 |
Missing Atoms: | 6 |
DFG conformation: | in |
αC-helix conformation: | in |
Salt bridge KIII.17 and EαC.24: | Yes (3Å) |
ASP rotation (xDFG.81) : | 349° |
PHE rotation (xDFG.82) : | 22° |
Activation loop position: | -2.9Å |
αC-helix position: | 17.1Å |
G-rich loop angle: | 45.2° |
G-rich loop distance: | 13.8Å |
G-rich loop rotation: | 63.2° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond ligand
H-bond protein
I5
H-bond ligand
H-bond protein
I9
H-bond ligand
H-bond protein
Binding pocket sequence
Uniprot | TLVGKGRFAEVYKVAVKIFSWKTEKDIFSDINENILQFLTAWLITAFHAKGNLQEYLTRGRPKMPIVHRDLKSSNILVLCDFGLS |
Structure: | TLVGKGRFAEVYKVAVKIFSWKTEKDIFSDINENILQFLTAWLITAFHAKGNLQEYLTRGRPKMPIVHRDLKSSNILVLCDFGLS |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: J2V
Ligand Name: N-{4-[3-(6-methoxypyridin-3-yl)-1H-pyrrolo[3,2-b]pyridin-2-yl]pyridin-2-yl}acetamide
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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 T 248 | 2 L 249 | 3 V 250 | 4 G 251 | 5 K 252 | 6 G 253 | 7 R 254 | 8 F 255 | 9 A 256 | 10 E 257 | 11 V 258 | 12 Y 259 | 13 K 260 | 14 V 274 | 15 A 275 | 16 V 276 | 17 K 277 | 18 I 278 | 19 F 279 | 20 S 286 |
■ | ■ | ■ | ■ | ■▲ | |||||||||||||||
αC | b.l | IV | |||||||||||||||||
21 W 287 | 22 K 288 | 23 T 289 | 24 E 290 | 25 K 291 | 26 D 292 | 27 I 293 | 28 F 294 | 29 S 295 | 30 D 296 | 31 I 297 | 32 N 298 | 33 E 302 | 34 N 303 | 35 I 304 | 36 L 305 | 37 Q 306 | 38 F 307 | 39 L 308 | 40 T 309 |
■ | ■ | ||||||||||||||||||
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 A 310 | 42 W 322 | 43 L 323 | 44 I 324 | 45 T 325 | 46 A 326 | 47 F 327 | 48 H 328 | 49 A 329 | 50 K 330 | 51 G 331 | 52 N 332 | 53 L 333 | 54 Q 334 | 55 E 335 | 56 Y 336 | 57 L 337 | 58 T 338 | 59 R 339 | 60 G 369 |
■ | ■ | ■♦ | ■▲▲ | ■ | ■ | ||||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 R 370 | 62 P 371 | 63 K 372 | 64 M 373 | 65 P 374 | 66 I 375 | 67 V 376 | 68 H 377 | 69 R 378 | 70 D 379 | 71 L 380 | 72 K 381 | 73 S 382 | 74 S 383 | 75 N 384 | 76 I 385 | 77 L 386 | 78 V 387 | 79 L 395 | 80 C 396 |
■ | ■ | ■ | |||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 397 | 82 F 398 | 83 G 399 | 84 L 400 | 85 S 401 | |||||||||||||||
■ |
Binding affinities
ChEMBL ID:CHEMBL4279160Bioaffinities: 2 records for 2 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | TGF-beta receptor type I | 8.5 | 8.5 | 8.5 | pIC50 | 1 |
Homo sapiens | TGF-beta receptor type II | 7.4 | 7.4 | 7.4 | pIC50 | 1 |