SMTL ID : 8pwe.1

Crystal structure of VDR complex with Novel Des-C-Ring and Aromatic-D-Ring analog 3a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-2-2-mer

Ligands

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 8 residues within 4Å: Chain A: T.23, Y.24, D.25, Y.28, Y.113, K.117, R.151 Ligands: FUW.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.24, A:Y.28 Hydrogen bonds: A:D.25 Salt bridges: A:K.117, A:R.151 ACT.3: 8 residues within 4Å: Chain C: T.23, Y.24, D.25, Y.28, Y.113, K.117, R.151 Ligands: FUW.4 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.24, C:Y.28 Hydrogen bonds: C:D.25, C:Y.113 Water bridges: C:D.25 Salt bridges: C:K.117, C:R.151

2 x FUW: (1~{R},3~{S},5~{Z})-4-methylidene-5-[(~{E})-3-[3-(6-methyl-6-oxidanyl-hept-3-ynyl)phenyl]pent-2-enylidene]cyclohexane-1,3-diol(Non-covalent)

FUW.2: 20 residues within 4Å: Chain A: Y.24, L.104, L.107, V.111, S.114, I.145, I.148, R.151, S.152, S.155, W.163, C.165, Y.172, V.177, A.180, H.182, L.190, H.272, L.279 Ligands: ACT.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.104, A:L.107, A:V.111, A:I.145, A:I.148, A:W.163, A:W.163, A:Y.172, A:V.177, A:L.190, A:L.279 Hydrogen bonds: A:Y.24, A:S.114, A:R.151, A:S.155, A:H.182 FUW.4: 20 residues within 4Å: Chain C: Y.24, L.104, L.107, V.111, S.114, I.145, I.148, R.151, S.152, S.155, W.163, C.165, Y.172, V.177, A.180, H.182, L.190, H.272, L.279 Ligands: ACT.3 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:L.104, C:L.107, C:V.111, C:I.145, C:I.148, C:W.163, C:W.163, C:Y.172, C:V.177, C:L.190, C:L.279 Hydrogen bonds: C:Y.24, C:Y.24, C:S.114, C:R.151, C:S.155, C:H.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zarate-Ruiz, A. et al., Further Studies on the Highly Active Des-C-Ring and Aromatic-D-Ring Analogues of 1 alpha ,25-Dihydroxyvitamin D 3 (Calcitriol): Refinement of the Side Chain. J.Med.Chem. (2023)

Release Date

2024-08-07

Peptides

Vitamin D3 receptor A: AC
Nuclear receptor coactivator 2: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Vitamin D3 receptor A

Nuclear receptor coactivator 2

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