SMTL ID : 5s85.1

XChem group deposition -- Crystal Structure of human ACVR1 in complex with FM000884c

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.33 Å

Oligo State

homo-dimer

Ligands

4 x LU8: 4-methyl-3-[4-(1-methylpiperidin-4-yl)phenyl]-5-(3,4,5-trimethoxyphenyl)pyridine(Non-covalent)

LU8.1: 16 residues within 4Å: Chain A: V.16, V.24, A.35, K.37, L.65, L.83, T.85, H.86, Y.87, H.88, G.91, K.142, N.143, L.145, A.155, D.156 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.16, A:V.16, A:A.35, A:Y.87, A:L.145, A:L.145 Hydrogen bonds: A:T.85, A:H.88 Water bridges: A:D.156 LU8.7: 11 residues within 4Å: Chain A: V.6, A.7, R.8, W.29, A.69 Chain B: D.71, T.73, Q.80, W.82 Ligands: LU8.8, EDO.17 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Q.80, B:W.82, B:W.82, A:V.6, A:R.8 Hydrogen bonds: A:A.7, A:R.8 LU8.8: 7 residues within 4Å: Chain A: W.29, I.68 Chain B: T.73, S.74, R.75, S.78 Ligands: LU8.7 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.29, B:R.75 LU8.21: 17 residues within 4Å: Chain B: V.16, A.35, K.37, E.50, L.83, T.85, H.86, Y.87, H.88, G.91, D.95, K.142, N.143, L.145, A.155, D.156 Ligands: XK4.25 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.16, B:V.16, B:A.35, B:Y.87, B:D.95, B:L.145 Hydrogen bonds: B:T.85, B:H.88 Salt bridges: B:D.95

13 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 9 residues within 4Å: Chain A: H.61, E.62, N.63, I.64, L.65, G.66, H.86, H.88, C.153 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.61, A:I.64, A:G.66, A:H.88, A:K.147 EDO.3: 6 residues within 4Å: Chain A: F.233, D.235, V.236, Q.255, R.256, N.258 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.258 Water bridges: A:F.233, A:N.258, A:N.258 EDO.4: 2 residues within 4Å: Chain A: R.247, V.252 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.247, A:R.247 EDO.5: 6 residues within 4Å: Chain A: R.182, F.233, Y.234, V.237, P.238, N.239 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.182, A:R.182, A:P.238 EDO.16: 6 residues within 4Å: Chain A: V.57, L.59, R.60, H.120, G.130, K.131 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.60, A:R.60, A:G.130 EDO.17: 4 residues within 4Å: Chain B: L.12, E.23, I.38 Ligands: LU8.7 No protein-ligand interaction detected (PLIP) EDO.18: 4 residues within 4Å: Chain A: N.223, I.225, R.262, S.265 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.223, A:S.265 Water bridges: A:S.222, A:R.262 EDO.19: 3 residues within 4Å: Chain A: G.19, R.20, Y.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.20, A:Y.21 EDO.20: 3 residues within 4Å: Chain A: R.218, K.230, Y.234 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.218, A:R.218 EDO.23: 6 residues within 4Å: Chain B: F.233, D.235, V.236, Q.255, R.256, N.258 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.258, B:N.258 Water bridges: B:F.233, B:Q.255, B:N.258, B:N.258 EDO.30: 9 residues within 4Å: Chain B: H.61, E.62, I.64, L.65, G.66, H.86, H.88, K.147, C.153 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.61, B:G.66 Water bridges: B:H.61 EDO.31: 3 residues within 4Å: Chain B: Y.281, Q.282, N.283 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.282, B:N.283 Water bridges: B:R.256 EDO.32: 2 residues within 4Å: Chain B: V.221, G.224 No protein-ligand interaction detected (PLIP)

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.6: 1 residues within 4Å: Chain B: R.75 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.75 DMS.24: 2 residues within 4Å: Chain B: R.292, K.295 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.292, B:R.292, B:K.295

7 x XK4: (3R)-1,2-oxazolidin-3-amine(Non-covalent)

XK4.9: 6 residues within 4Å: Chain A: T.56, V.57, G.127, G.130, K.131, P.132 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.57 Hydrogen bonds: A:T.56, A:G.127, A:G.130 Water bridges: A:M.58 XK4.10: 3 residues within 4Å: Chain A: V.178, K.181, F.243 No protein-ligand interaction detected (PLIP) XK4.11: 5 residues within 4Å: Chain A: R.49, E.52, A.160, V.161, M.162 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.49, A:R.49, A:M.162, A:M.162 XK4.12: 6 residues within 4Å: Chain A: K.202, R.203, I.206, R.287, L.288, T.289 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.202 Hydrogen bonds: A:R.287 Water bridges: A:K.202 XK4.25: 5 residues within 4Å: Chain B: E.14, V.16, Y.87, E.89 Ligands: LU8.21 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.87 XK4.26: 4 residues within 4Å: Chain B: H.163, N.168, L.170, D.196 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.196 Water bridges: B:D.196, B:D.196 XK4.27: 9 residues within 4Å: Chain B: D.199, K.202, R.203, I.206, P.284, S.285, R.287, L.288, T.289 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.203, B:I.206 Hydrogen bonds: B:R.203, B:R.287 Water bridges: B:K.202

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.13: 3 residues within 4Å: Chain A: H.88, K.147, K.148 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.148 Water bridges: A:E.89, A:N.149 Salt bridges: A:H.88 SO4.14: 2 residues within 4Å: Chain A: P.260, N.261 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.261 Water bridges: A:R.262 SO4.15: 4 residues within 4Å: Chain A: R.182, N.239, D.240, P.241 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.240, A:D.240 Water bridges: A:R.182, A:R.182 Salt bridges: A:R.182 SO4.22: 3 residues within 4Å: Chain B: H.88, K.147, K.148 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.148 Water bridges: B:E.89, B:V.146, B:N.149 Salt bridges: B:H.88 SO4.28: 3 residues within 4Å: Chain B: G.19, R.20, Y.21 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.20 SO4.29: 2 residues within 4Å: Chain B: T.180, K.181 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.181 Water bridges: B:K.140, B:T.180, B:T.180, B:R.182, B:D.240, B:D.240 Salt bridges: B:K.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, E.P. et al., XChem group deposition. To Be Published

Release Date

2021-06-23

Peptides

Activin receptor type-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Activin receptor type-1

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