SMTL ID : 6y6o.1

Structure of mature activin A with small molecule 42

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: Y.39, C.40, C.81, P.83 Chain B: H.59, I.63, L.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.40 SO4.2: 4 residues within 4Å: Chain A: H.65, M.68, R.69 Chain B: W.25 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:W.25 Salt bridges: A:H.65, A:R.69 SO4.3: 3 residues within 4Å: Chain A: G.1, G.53, S.54 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.54, A:S.54, A:S.54 Water bridges: A:G.1 SO4.4: 4 residues within 4Å: Chain A: K.7, V.8, N.9, I.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.9, A:I.10 SO4.6: 7 residues within 4Å: Chain B: K.7, V.8 Chain C: N.26, D.27, W.28, I.30, Y.94 No protein-ligand interaction detected (PLIP) SO4.7: 7 residues within 4Å: Chain C: Y.39, C.40, C.81, P.83 Chain D: H.59, I.63, L.77 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:C.40 SO4.8: 4 residues within 4Å: Chain C: H.65, M.68, R.69 Chain D: W.25 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Salt bridges: C:H.65, C:R.69 Hydrogen bonds: D:W.25 SO4.9: 3 residues within 4Å: Chain C: G.1, G.53, S.54 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.54, C:S.54, C:S.54 Water bridges: C:G.1 SO4.10: 4 residues within 4Å: Chain C: K.7, V.8, N.9, I.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.9, C:I.10 SO4.12: 7 residues within 4Å: Chain A: N.26, D.27, W.28, I.30, Y.94 Chain D: K.7, V.8 No protein-ligand interaction detected (PLIP)

2 x OCK: (3~{R})-4-ethyl-3-methyl-3-propyl-1~{H}-1,4-benzodiazepine-2,5-dione(Non-covalent)

OCK.5: 7 residues within 4Å: Chain A: W.25, W.28, I.29, M.91, Y.93, I.105 Chain B: F.58 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.25, A:W.25, A:Y.93, A:I.105, B:F.58, B:F.58 OCK.11: 7 residues within 4Å: Chain C: W.25, W.28, I.29, M.91, Y.93, I.105 Chain D: F.58 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:W.25, C:W.25, C:Y.93, C:I.105, D:F.58, D:F.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kidd, S.L. et al., Demonstration of the utility of DOS-derived fragment libraries for rapid hit derivatisation in a multidirectional fashion. Chem Sci (2020)

Release Date

2021-02-03

Peptides

Inhibin beta A chain: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Inhibin beta A chain

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