SMTL ID : 4jyi.1

Crystal structure of RARbeta LBD in complex with selective partial agonist BMS641 [3-chloro-4-[(E)-2-(5,5-dimethyl-8-phenyl-5,6-dihydronaphthalen-2-yl)ethenyl]benzoic acid]

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-2-mer

Ligands

2 x JYI: 3-chloro-4-[(E)-2-(5,5-dimethyl-8-phenyl-5,6-dihydronaphthalen-2-yl)ethenyl]benzoic acid(Non-covalent)

JYI.1: 16 residues within 4Å: Chain A: F.45, W.71, F.74, L.77, A.78, C.81, L.112, L.115, I.116, I.119, R.122, F.132, S.133, F.148, G.237, I.256 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.71, A:F.74, A:F.74, A:L.115, A:L.115, A:I.116, A:I.119, A:F.132, A:F.148, A:I.256 Hydrogen bonds: A:S.133 Salt bridges: A:R.122 Halogen bonds: A:F.74 JYI.2: 18 residues within 4Å: Chain B: F.45, W.71, F.74, L.77, A.78, C.81, L.112, L.115, I.116, I.119, R.122, F.132, S.133, F.148, G.237, V.241, L.244, I.256 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:W.71, B:F.74, B:L.112, B:L.115, B:L.115, B:I.116, B:I.119, B:F.132, B:F.148, B:F.148, B:V.241, B:L.244, B:I.256 Hydrogen bonds: B:S.133 Salt bridges: B:R.122 pi-Stacking: B:F.74 Halogen bonds: B:F.74

1 x FLC: CITRATE ANION(Non-covalent)

FLC.3: 5 residues within 4Å: Chain A: P.254 Chain D: H.2, K.3, I.4, R.7 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.3, D:I.4 Salt bridges: D:H.2, D:R.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nadendla, E. et al., An Unexpected Mode Of Binding Defines BMS948 as A Full Retinoic Acid Receptor beta (RAR beta , NR1B2) Selective Agonist. Plos One (2015)

Release Date

2014-03-19

Peptides

Retinoic acid receptor beta: AB
Nuclear receptor coactivator 1: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
F

D
G

Retinoic acid receptor beta

Nuclear receptor coactivator 1

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