SMTL ID : 4jyg.1

Crystal structure of RARbeta LBD in complex with agonist BMS411 [4-{[(5,5-dimethyl-8-phenyl-5,6-dihydronaphthalen-2-yl)carbonyl]amino}benzoic acid]

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-2-2-mer

Ligands

2 x 1NY: 4-{[(5,5-dimethyl-8-phenyl-5,6-dihydronaphthalen-2-yl)carbonyl]amino}benzoic acid(Non-covalent)

1NY.1: 19 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, V.155, G.237, V.241, L.244, I.256 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:W.71, A:F.74, A:A.78, A:L.112, A:L.115, A:I.116, A:I.119, A:I.119, A:I.119, A:F.132, A:F.148, A:F.148, A:F.148, A:V.155, A:V.241, A:L.244, A:I.256 Hydrogen bonds: A:L.77, A:L.115, A:S.133 Salt bridges: A:R.122 1NY.3: 18 residues within 4Å: Chain B: F.45, W.71, F.74, L.77, A.78, C.81, L.115, I.116, I.119, R.122, F.132, S.133, F.148, V.155, 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:F.74, B:L.115, B:I.116, B:I.116, B:I.119, B:I.119, B:F.132, B:F.132, B:V.155, B:V.241, B:L.244, B:I.256 Hydrogen bonds: B:L.115, B:S.133 Salt bridges: B:R.122

1 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.2: 5 residues within 4Å: Chain B: T.56, R.65, L.66, L.68, G.69 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.69 Water bridges: B:R.65

1 x FLC: CITRATE ANION(Non-covalent)

FLC.4: 5 residues within 4Å: Chain A: P.254 Chain D: H.2, K.3, I.4, R.7 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:K.3 Hydrogen bonds: D:K.3, D:K.3, D:I.4 Water bridges: D:H.2 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
Steroid Receptor Coactivator 1: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
F

D
G

Retinoic acid receptor beta

Steroid Receptor Coactivator 1

Related Entries With Identical Sequence