SMTL ID : 7b39.1

Allene-Based Design of a Noncalcemic Vitamin D Receptor Agonist

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

hetero-2-2-mer

Ligands

2 x T0H: (1R,3S,Z)-5-(2-((3aS,7aS,E)-1-(6-hydroxy-6-methylhept-1-en-1-ylidene)-7a-methyloctahydro-4H-inden-4-ylidene)ethylidene)-4-methylenecyclohexane-1,3-diol(Non-covalent)

T0H.1: 18 residues within 4Å: Chain A: Y.24, V.111, S.114, I.148, M.149, R.151, S.152, S.155, W.163, C.165, V.177, A.180, H.182, L.190, H.272, Y.276, L.279 Ligands: ACT.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.24, A:I.148, A:W.163, A:V.177, A:V.177, A:L.190, A:L.279 Hydrogen bonds: A:Y.24, A:Y.24, A:S.114, A:R.151, A:R.151, A:H.182 T0H.3: 18 residues within 4Å: Chain C: Y.24, V.111, S.114, I.148, M.149, R.151, S.152, S.155, W.163, C.165, V.177, A.180, H.182, L.190, H.272, Y.276, L.279 Ligands: ACT.4 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:Y.24, C:I.148, C:W.163, C:V.177, C:V.177, C:L.190, C:L.279 Hydrogen bonds: C:Y.24, C:S.114, C:R.151, C:R.151, C:H.182

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

ACT.2: 8 residues within 4Å: Chain A: T.23, Y.24, D.25, Y.28, Y.113, K.117, R.151 Ligands: T0H.1 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.4: 8 residues within 4Å: Chain C: T.23, Y.24, D.25, Y.28, Y.113, K.117, R.151 Ligands: T0H.3 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Y.24, C:Y.28 Hydrogen bonds: C:D.25, C:Y.113 Salt bridges: C:K.117, C:R.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fraga, R. et al., Design, Synthesis, Evaluation and Structure of Allenic 1 alpha ,25-Dihydroxyvitamin D 3 Analogs with Locked Mobility at C-17. Chemistry (2021)

Release Date

2021-09-01

Peptides

Vitamin D3 receptor A: AC
Nuclear receptor coactivator 1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Vitamin D3 receptor A

Nuclear receptor coactivator 1

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