SMTL ID : 6dtp.1

CRYSTAL STRUCTURE OF HUMAN 17BETA-HYDROXYSTEROID DEHYDROGENASE TYPE 1 COMPLEXED WITH EM139

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: C.55, P.56, P.57, G.58, S.59, L.60 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.58, A:S.59, A:S.59, A:L.60 GOL.2: 10 residues within 4Å: Chain A: G.146, F.161, E.164, R.267 Chain B: G.146, L.147, F.161, R.267 Ligands: GOL.4, EDO.6 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.146, B:R.267, A:G.146, A:R.267, A:R.267 Water bridges: B:R.267, B:R.267 GOL.3: 4 residues within 4Å: Chain A: V.240, T.243, Y.254, F.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.243, A:T.243, A:F.255 GOL.4: 6 residues within 4Å: Chain A: R.267, D.270, P.271 Chain B: L.147, R.253 Ligands: GOL.2 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.267, A:R.267, A:R.267, A:P.271, B:R.253 GOL.5: 10 residues within 4Å: Chain A: C.90, N.91, A.92, G.93, N.115, T.119, V.140, T.141, K.160, L.163 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.90, A:N.115 Water bridges: A:T.9 GOL.10: 3 residues within 4Å: Chain B: F.255, T.256, T.257 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.256 GOL.11: 4 residues within 4Å: Chain B: A.231, Q.232, N.233, E.236 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.232, B:N.233, B:N.233, B:E.236

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 5 residues within 4Å: Chain A: R.253 Chain B: R.267, D.270, P.271 Ligands: GOL.2 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:R.253 Hydrogen bonds: B:R.267, B:R.267, B:D.270 EDO.7: 4 residues within 4Å: Chain A: D.26, S.28, S.30, R.246 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.28, A:S.30, A:S.30, A:R.246, A:R.246 EDO.12: 3 residues within 4Å: Chain B: Y.217, A.221, K.224 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.224 EDO.13: 3 residues within 4Å: Chain B: R.77, F.126, D.129 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.126 Water bridges: B:D.129

1 x EM9: N-butyl-11-[(7alpha,9beta,13alpha,14beta,16alpha,17alpha)-16-chloro-3,17-dihydroxyestra-1,3,5(10)-trien-7-yl]-N-methylundecanamide(Non-covalent)

EM9.8: 13 residues within 4Å: Chain A: S.143, V.144, G.145, L.150, Y.156, G.187, P.188, Y.219, H.222, S.223, F.227, M.280, E.283 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.144, A:L.150, A:Y.219, A:F.227 Hydrogen bonds: A:S.143, A:S.143, A:Y.156, A:H.222, A:E.283

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 11 residues within 4Å: Chain A: A.171, L.174, L.175, V.179, H.180, L.181, P.250, T.251, L.252 Chain B: S.274, T.278 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.174, A:L.181

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.14: 4 residues within 4Å: Chain A: K.131, P.176, F.177 Chain B: R.215 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.215, B:R.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, T. et al., CRYSTAL STRUCTURE OF HUMAN 17BETA-HYDROXYSTEROID DEHYDROGENASE TYPE 1 COMPLEXED WITH Dual-Site Inhibitor EM-139. Health (2018)

Release Date

2018-09-12

Peptides

Estradiol 17-beta-dehydrogenase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Estradiol 17-beta-dehydrogenase 1

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