SMTL ID : 8ck5.1

VDR LBD complex with 25-nitro derivative of 1,25D3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

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

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

1 x UYO: (1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methyl-6-nitro-heptan-2-yl]-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol(Non-covalent)

UYO.2: 20 residues within 4Å: Chain A: Y.24, L.107, A.108, L.110, V.111, S.114, I.148, R.151, S.152, S.155, W.163, C.165, V.177, A.180, H.182, L.186, L.190, H.272, Y.276, L.279 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.107, A:L.107, A:L.110, A:L.110, A:I.148, A:W.163, A:V.177, A:L.186, A:L.190 Hydrogen bonds: A:Y.24, A:S.114, A:R.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gomez-Bouzo, U. et al., Structural analysis and biological activities of C25-amino and C25-nitro vitamin D analogs. Bioorg.Chem. (2023)

Release Date

2023-04-26

Peptides

Vitamin D3 receptor A: A
Nuclear receptor coactivator 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Vitamin D3 receptor A

Nuclear receptor coactivator 1

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