SMTL ID : 5s7y.1

XChem group deposition -- Crystal Structure of human ACVR1 in complex with FM010933a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 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 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: 12 residues within 4Å: Chain A: R.4, V.6, A.7, R.8, W.29, A.69 Chain B: D.71, T.73, Q.80, W.82 Ligands: LU8.8, EDO.13 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:R.8, A:W.29, B:Q.80, B:W.82 Water bridges: A:A.7 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 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:R.4 pi-Stacking: A:W.29 Hydrophobic interactions: B:R.75 LU8.17: 17 residues within 4Å: Chain B: V.16, V.24, 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 11 PLIP interactions: 11 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 Water bridges: B:K.37 Salt bridges: B:D.95

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

EDO.2: 8 residues within 4Å: Chain A: H.61, E.62, I.64, L.65, G.66, H.86, H.88, C.153 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.66, A:H.88 Water bridges: A:K.147 EDO.3: 7 residues within 4Å: Chain A: F.233, D.235, V.236, Q.255, R.256, P.257, 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.12: 7 residues within 4Å: Chain A: V.57, M.58, 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.13: 6 residues within 4Å: Chain A: R.4 Chain B: L.12, E.23, W.25, I.38 Ligands: LU8.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.4 EDO.14: 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.15: 3 residues within 4Å: Chain A: G.19, R.20, Y.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.20 EDO.16: 3 residues within 4Å: Chain A: R.218, K.230, Y.234 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.218, A:R.218 Water bridges: A:Y.234 EDO.19: 7 residues within 4Å: Chain B: F.233, D.235, V.236, Q.255, R.256, N.258 Ligands: XJP.23 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.258, B:N.258 Water bridges: B:F.233, B:Q.255, B:N.258 EDO.29: 9 residues within 4Å: Chain B: H.61, E.62, I.64, L.65, G.66, H.86, H.88, K.147, C.153 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.61, B:G.66, B:H.86, B:H.88 Water bridges: B:H.61 EDO.30: 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.31: 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.20: 2 residues within 4Å: Chain B: R.292, K.295 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.292

7 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.240, A:D.240 Water bridges: A:R.182, A:R.182, A:N.239 Salt bridges: A:R.182 SO4.18: 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 SO4.26: 3 residues within 4Å: Chain B: G.19, R.20, Y.21 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.20 Water bridges: B:K.142, B:K.142 SO4.27: 2 residues within 4Å: Chain B: T.180, K.181 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.181 Water bridges: B:T.180, B:R.182 Salt bridges: B:K.181 SO4.28: 3 residues within 4Å: Chain B: S.242, E.244, D.245 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.242, B:S.242, B:E.244

5 x XJP: (2S,4R)-1,3-thiazolidine-2,4-diamine(Non-covalent)

XJP.21: 3 residues within 4Å: Chain B: V.178, E.191, F.243 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.191 Water bridges: B:K.181, B:K.181 XJP.22: 6 residues within 4Å: Chain A: E.44, K.45, F.48 Chain B: E.52, N.55, D.171 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.52, B:D.171, A:E.44 Water bridges: B:R.49, B:N.55, B:N.55 XJP.23: 5 residues within 4Å: Chain B: Q.254, Q.255, R.256, N.258 Ligands: EDO.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.256, B:N.258, B:N.258 XJP.24: 2 residues within 4Å: Chain B: N.239, D.240 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.239 XJP.25: 5 residues within 4Å: Chain B: W.29, Q.30, E.32, V.34, I.68 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.29, B:E.32

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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