SMTL ID : 5s7q.1

XChem group deposition -- Crystal Structure of human ACVR1 in complex with FM010944a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 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.83, T.85, H.86, Y.87, H.88, E.89, G.91, K.142, N.143, L.145, A.155, D.156 8 PLIP interactions: 8 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 LU8.7: 14 residues within 4Å: Chain A: R.4, V.6, A.7, R.8, W.29, I.68, D.71 Chain B: R.8, D.71, T.73, Q.80, W.82 Ligands: LU8.8, EDO.13 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.73, B:Q.80, B:W.82, A:V.6, A:R.8 Hydrogen bonds: A:A.7 LU8.8: 9 residues within 4Å: Chain A: R.4, W.29, E.32, I.68 Chain B: T.73, S.74, R.75, S.78 Ligands: LU8.7 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:R.75, A:W.29 Water bridges: B:R.75 Hydrogen bonds: A:R.4 LU8.18: 17 residues within 4Å: Chain B: V.16, V.24, A.35, K.37, E.50, L.65, L.83, T.85, Y.87, H.88, G.91, D.95, K.142, N.143, L.145, A.155, D.156 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.16, B:V.16, B:V.24, 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 Water bridges: A:H.61 EDO.3: 6 residues within 4Å: Chain A: F.233, D.235, V.236, Q.255, R.256, N.258 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.258, 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.182, A:R.182 EDO.12: 4 residues within 4Å: Chain A: V.57, M.58, G.130, K.131 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.58 EDO.13: 4 residues within 4Å: Chain B: L.12, I.38, W.82 Ligands: LU8.7 No protein-ligand interaction detected (PLIP) EDO.14: 3 residues within 4Å: Chain A: N.223, I.225, S.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.223, A:S.265 EDO.15: 2 residues within 4Å: Chain A: R.20, Y.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.20, A:Y.21 EDO.16: 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.20: 7 residues within 4Å: Chain B: F.233, D.235, V.236, Q.255, R.256, P.257, N.258 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.258, B:N.258 Water bridges: B:F.233, B:N.258, B:N.258 EDO.25: 6 residues within 4Å: Chain B: I.64, L.65, G.66, H.86, H.88, C.153 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.66, B:H.88 Water bridges: B:Y.87 EDO.26: 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.27: 2 residues within 4Å: Chain B: V.221, G.224 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.224, B:V.226

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

DMS.6: 2 residues within 4Å: Chain A: H.86 Chain B: R.75 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.75 Salt bridges: A:E.32 DMS.21: 1 residues within 4Å: Chain B: K.295 No protein-ligand interaction detected (PLIP)

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

SO4.9: 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 SO4.10: 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 SO4.11: 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:K.142, A:K.142 Salt bridges: A:R.182 SO4.19: 3 residues within 4Å: Chain B: H.88, K.147, K.148 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.148 Water bridges: B:E.89, B:N.149 Salt bridges: B:H.88 SO4.23: 3 residues within 4Å: Chain B: G.19, R.20, Y.21 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.20, B:Y.21 SO4.24: 3 residues within 4Å: Chain B: G.179, T.180, K.181 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.179, B:K.181 Water bridges: B:K.140, B:K.140, B:D.240 Salt bridges: B:K.181

2 x XJM: 5-methyl-1H-tetrazole(Non-covalent)

XJM.17: 1 residues within 4Å: Chain B: E.191 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.191 XJM.22: 7 residues within 4Å: Chain B: P.132, M.162, H.163, S.164, Q.169, L.170, D.171 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.164, B:D.171

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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