3MY0 - chain R | Activin A receptor type IL
Structure information
PDB: | 3MY0 |
PubMed: | 25557927 |
Release date: | 2010-07-21 |
Resolution: | 2.65 Å |
Kinase: | ACVRL1 (ALK1) |
Family: | STKR |
Group: | TKL |
Species: | HUMAN |
Quality Score: | 8 |
Missing Residues: | 0 |
Missing Atoms: | 34 |
DFG conformation: | in |
αC-helix conformation: | in |
Salt bridge KIII.17 and EαC.24: | No (4.6Å) |
ASP rotation (xDFG.81) : | 347° |
PHE rotation (xDFG.82) : | 2° |
Activation loop position: | -3.4Å |
αC-helix position: | 17.2Å |
G-rich loop angle: | 53.8° |
G-rich loop distance: | 16.6Å |
G-rich loop rotation: | 43.4° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
No waters were found in the defined clusters
Binding pocket sequence
Uniprot | ECVGKGRYGEVWRVAVKIFSWFRETEIYNTVLDNILGFIASWLITHYHEHGSLYDFLQRTQGKPAIAHRDFKSRNVLVIADLGLA |
Structure: | ECVGKGRYGEVWRVAVKIFSWFRETEIYNTVLDNILGFIASWLITHYHEHGSLYDFLQRTQGKPAIAHRDFKSRNVLVIADLGLA |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: LDN
Ligand Name: 4-[6-(4-piperazin-1-ylphenyl)pyrazolo[1,5-a]pyrimidin-3-yl]quinoline
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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 E 206 | 2 C 207 | 3 V 208 | 4 G 209 | 5 K 210 | 6 G 211 | 7 R 212 | 8 Y 213 | 9 G 214 | 10 E 215 | 11 V 216 | 12 W 217 | 13 R 218 | 14 V 226 | 15 A 227 | 16 V 228 | 17 K 229 | 18 I 230 | 19 F 231 | 20 S 238 |
■ | ■ | ■ | ■ | ||||||||||||||||
αC | b.l | IV | |||||||||||||||||
21 W 239 | 22 F 240 | 23 R 241 | 24 E 242 | 25 T 243 | 26 E 244 | 27 I 245 | 28 Y 246 | 29 N 247 | 30 T 248 | 31 V 249 | 32 L 250 | 33 D 254 | 34 N 255 | 35 I 256 | 36 L 257 | 37 G 258 | 38 F 259 | 39 I 260 | 40 A 261 |
■ | |||||||||||||||||||
IV | V | GK | hinge | linker | αD | αE | |||||||||||||
41 S 262 | 42 W 274 | 43 L 275 | 44 I 276 | 45 T 277 | 46 H 278 | 47 Y 279 | 48 H 280 | 49 E 281 | 50 H 282 | 51 G 283 | 52 S 284 | 53 L 285 | 54 Y 286 | 55 D 287 | 56 F 288 | 57 L 289 | 58 Q 290 | 59 R 291 | 60 T 320 |
■ | ■ | ■♦ | ■▲ | ■ | ■ | ■ | ■ | ||||||||||||
αE | VI | c.l | VII | VIII | x | ||||||||||||||
61 Q 321 | 62 G 322 | 63 K 323 | 64 P 324 | 65 A 325 | 66 I 326 | 67 A 327 | 68 H 328 | 69 R 329 | 70 D 330 | 71 F 331 | 72 K 332 | 73 S 333 | 74 R 334 | 75 N 335 | 76 V 336 | 77 L 337 | 78 V 338 | 79 I 346 | 80 A 347 |
■ | ■ | ■ | |||||||||||||||||
DFG | a.l | ||||||||||||||||||
81 D 348 | 82 L 349 | 83 G 350 | 84 L 351 | 85 A 352 | |||||||||||||||
■ |
Binding affinities
ChEMBL ID:CHEMBL513147Bioaffinities: 30 records for 11 kinase(s)
Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
---|---|---|---|---|---|---|
Homo sapiens | Activin receptor type-1 | 7.8 | 7.4 | 8.5 | pIC50 | 6 |
Mus musculus | Activin receptor type-1 | 7.9 | 7.9 | 7.9 | pEC50 | 1 |
Homo sapiens | Activin receptor type-1B | 6.5 | 5.7 | 7.4 | pIC50 | 3 |
Homo sapiens | AMP-activated protein kinase, beta-1 subunit | 6 | 6 | 6 | pIC50 | 1 |
Homo sapiens | Bone morphogenetic protein receptor type-1A | 7.7 | 7.6 | 8.7 | pIC50 | 3 |
Homo sapiens | Bone morphogenetic protein receptor type-1B | 7.9 | 7.2 | 9 | pIC50 | 3 |
Homo sapiens | Bone morphogenetic protein receptor type-2 | 5.4 | 5.4 | 5.4 | pIC50 | 1 |
Homo sapiens | Serine/threonine-protein kinase receptor R3 | 7.9 | 7.7 | 8 | pIC50 | 3 |
Homo sapiens | TGF-beta receptor type I | 6.3 | 6.3 | 7.6 | pIC50 | 6 |
Homo sapiens | TGF-beta receptor type II | 6.8 | 6.8 | 6.9 | pIC50 | 2 |
Homo sapiens | Vascular endothelial growth factor receptor 2 | 6.7 | 6.7 | 6.7 | pIC50 | 1 |