SMTL ID : 5en4.1

Complex of 17-beta-hydroxysteroid dehydrogenase type 14 with inhibitor.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 31 residues within 4Å: Chain A: G.16, G.18, R.19, G.20, I.21, G.22, D.40, K.41, D.42, C.61, D.62, V.63, T.64, N.89, A.90, G.91, L.113, I.139, S.140, S.141, Y.154, K.158, P.184, G.185, N.186, I.187, T.189, P.190, L.191, W.192 Ligands: 5Q6.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:P.184 Hydrogen bonds: A:G.16, A:G.18, A:R.19, A:I.21, A:K.41, A:D.62, A:D.62, A:V.63, A:N.89, A:K.158, A:I.187, A:I.187, A:T.189, A:L.191 Water bridges: A:G.22, A:D.40, A:D.42, A:T.64, A:N.89 Salt bridges: A:R.19 NAD.4: 31 residues within 4Å: Chain B: G.16, G.18, R.19, G.20, I.21, G.22, D.40, K.41, D.42, C.61, D.62, V.63, T.64, N.89, A.90, G.91, L.113, I.139, S.140, S.141, Y.154, K.158, P.184, G.185, N.186, I.187, T.189, P.190, L.191, W.192 Ligands: 5Q6.5 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:P.184 Hydrogen bonds: B:G.16, B:G.18, B:R.19, B:I.21, B:K.41, B:D.62, B:D.62, B:V.63, B:N.89, B:K.158, B:I.187, B:I.187, B:T.189, B:L.191 Water bridges: B:G.22, B:D.40, B:D.42, B:T.64, B:N.89 Salt bridges: B:R.19 NAD.7: 31 residues within 4Å: Chain C: G.16, G.18, R.19, G.20, I.21, G.22, D.40, K.41, D.42, C.61, D.62, V.63, T.64, N.89, A.90, G.91, L.113, I.139, S.140, S.141, Y.154, K.158, P.184, G.185, N.186, I.187, T.189, P.190, L.191, W.192 Ligands: 5Q6.8 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:P.184 Hydrogen bonds: C:G.16, C:G.18, C:R.19, C:I.21, C:K.41, C:D.62, C:V.63, C:N.89, C:K.158, C:I.187, C:I.187, C:T.189, C:L.191 Water bridges: C:G.22, C:D.40, C:D.40, C:T.64, C:N.89 Salt bridges: C:R.19 NAD.10: 31 residues within 4Å: Chain D: G.16, G.18, R.19, G.20, I.21, G.22, D.40, K.41, D.42, C.61, D.62, V.63, T.64, N.89, A.90, G.91, L.113, I.139, S.140, S.141, Y.154, K.158, P.184, G.185, N.186, I.187, T.189, P.190, L.191, W.192 Ligands: 5Q6.11 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:P.184 Hydrogen bonds: D:G.16, D:G.18, D:R.19, D:I.21, D:K.41, D:D.62, D:V.63, D:N.89, D:K.158, D:I.187, D:I.187, D:T.189, D:L.191 Water bridges: D:G.22, D:D.40, D:D.40, D:T.64, D:N.89 Salt bridges: D:R.19

4 x 5Q6: [2,3-bis(oxidanyl)phenyl]-[6-(2-fluoranyl-3-oxidanyl-phenyl)pyridin-2-yl]methanone(Non-covalent)

5Q6.2: 15 residues within 4Å: Chain A: H.93, P.96, S.141, V.143, Q.148, A.149, Q.150, A.151, Y.154, N.186, L.191, W.192, L.195 Chain D: Y.253 Ligands: NAD.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.143, A:Q.148, A:W.192, A:L.195, A:L.195 Hydrogen bonds: A:S.141, A:Q.148, A:Y.154 Water bridges: A:H.93, A:P.95 pi-Stacking: A:H.93 5Q6.5: 15 residues within 4Å: Chain B: H.93, P.96, S.141, V.143, Q.148, A.149, Q.150, A.151, Y.154, N.186, L.191, W.192, L.195 Chain C: Y.253 Ligands: NAD.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.143, B:Q.148, B:W.192, B:L.195, B:L.195 Hydrogen bonds: B:S.141, B:Q.148, B:Y.154 Water bridges: B:H.93, B:P.95 pi-Stacking: B:H.93 5Q6.8: 15 residues within 4Å: Chain B: Y.253 Chain C: H.93, P.96, S.141, V.143, Q.148, A.149, Q.150, A.151, Y.154, N.186, L.191, W.192, L.195 Ligands: NAD.7 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:V.143, C:Q.148, C:W.192, C:L.195, C:L.195 Hydrogen bonds: C:S.141, C:Q.148, C:Y.154 Water bridges: C:H.93, C:P.95 pi-Stacking: C:H.93 5Q6.11: 15 residues within 4Å: Chain A: Y.253 Chain D: H.93, P.96, S.141, V.143, Q.148, A.149, Q.150, A.151, Y.154, N.186, L.191, W.192, L.195 Ligands: NAD.10 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:V.143, D:Q.148, D:W.192, D:L.195, D:L.195 Hydrogen bonds: D:S.141, D:Q.148, D:Y.154 Water bridges: D:H.93, D:P.95 pi-Stacking: D:H.93

4 x NA: SODIUM ION(Non-functional Binders)

NA.3: 5 residues within 4Å: Chain A: E.50, L.53, P.54, G.55, A.56 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.53, A:A.56 NA.6: 5 residues within 4Å: Chain B: E.50, L.53, P.54, G.55, A.56 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.50, B:A.56 NA.9: 5 residues within 4Å: Chain C: E.50, L.53, P.54, G.55, A.56 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.50, C:A.56 NA.12: 5 residues within 4Å: Chain D: E.50, L.53, P.54, G.55, A.56 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.53, D:A.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Braun, F. et al., First Structure-Activity Relationship of 17 beta-Hydroxysteroid Dehydrogenase Type 14 Nonsteroidal Inhibitors and Crystal Structures in Complex with the Enzyme. J. Med. Chem. (2016)

Release Date

2016-11-23

Peptides

17-beta-hydroxysteroid dehydrogenase 14: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

17-beta-hydroxysteroid dehydrogenase 14