SMTL ID : 6p2b.1

Tethered PXR-LBD/SRC-1p bound to Garcinoic Acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x NQD: (2Z,6E,10E)-13-[(2R)-6-hydroxy-2,8-dimethyl-3,4-dihydro-2H-1-benzopyran-2-yl]-2,6,10-trimethyltrideca-2,6,10-trienoic acid(Non-covalent)

NQD.1: 18 residues within 4Å: Chain A: L.88, L.91, L.122, M.125, A.126, M.128, S.129, Q.167, F.170, W.181, M.205, H.209, H.289, R.292, L.293, I.296, F.302, M.307 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.88, A:M.125, A:F.170, A:F.170, A:W.181, A:W.181, A:W.181, A:L.293, A:I.296, A:F.302, A:F.302 Hydrogen bonds: A:S.129, A:S.129, A:Q.167 Salt bridges: A:H.289 NQD.3: 14 residues within 4Å: Chain B: L.91, M.125, A.126, M.128, S.129, Q.167, F.170, W.181, H.209, H.289, L.293, I.296, F.302, M.307 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.91, B:M.125, B:F.170, B:F.170, B:W.181, B:W.181, B:W.181, B:L.293, B:I.296, B:F.302, B:F.302 Hydrogen bonds: B:M.125, B:S.129, B:Q.167 Salt bridges: B:H.289

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 6 residues within 4Å: Chain A: T.172, K.213, L.217, H.218, E.219, Y.222 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.219 DMS.4: 5 residues within 4Å: Chain B: T.172, K.213, L.217, H.218, E.219 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.219 DMS.5: 6 residues within 4Å: Chain A: L.56, V.59, W.105 Chain B: L.56, V.59, W.105 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A pi-Cation interactions: B:W.105, B:W.105, A:W.105, A:W.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bartolini, D. et al., Garcinoic Acid Is a Natural and Selective Agonist of Pregnane X Receptor. J.Med.Chem. (2020)

Release Date

2020-04-01

Peptides

Nuclear receptor subfamily 1 group I member 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nuclear receptor subfamily 1 group I member 2

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