SMTL ID : 5o6o.1

17beta-hydroxysteroid dehydrogenase 14 variant T205 in complex with a non-steroidal 2,6-pyridinketone inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 31 residues within 4Å: Chain A: G.18, G.20, R.21, G.22, I.23, G.24, D.42, K.43, D.44, C.63, D.64, V.65, T.66, N.91, A.92, G.93, L.115, I.141, S.142, S.143, Y.156, K.160, P.186, G.187, N.188, I.189, T.191, P.192, L.193, W.194 Ligands: 9MB.4 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:P.186 Hydrogen bonds: A:G.18, A:G.20, A:R.21, A:I.23, A:K.43, A:K.43, A:D.44, A:D.44, A:D.64, A:D.64, A:V.65, A:N.91, A:K.160, A:I.189, A:I.189, A:T.191, A:L.193 Water bridges: A:G.24, A:N.91 Salt bridges: A:R.21 pi-Cation interactions: A:K.43 NAD.5: 31 residues within 4Å: Chain B: G.18, G.20, R.21, G.22, I.23, G.24, D.42, K.43, D.44, C.63, D.64, V.65, T.66, N.91, A.92, G.93, L.115, I.141, S.142, S.143, Y.156, K.160, P.186, G.187, N.188, I.189, T.191, P.192, L.193, W.194 Ligands: 9MB.8 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:P.186 Hydrogen bonds: B:G.18, B:G.20, B:R.21, B:I.23, B:K.43, B:K.43, B:D.44, B:D.44, B:D.64, B:D.64, B:V.65, B:N.91, B:K.160, B:I.189, B:I.189, B:T.191, B:L.193 Water bridges: B:G.24, B:N.91 Salt bridges: B:R.21 pi-Cation interactions: B:K.43 NAD.9: 31 residues within 4Å: Chain C: G.18, G.20, R.21, G.22, I.23, G.24, D.42, K.43, D.44, C.63, D.64, V.65, T.66, N.91, A.92, G.93, L.115, I.141, S.142, S.143, Y.156, K.160, P.186, G.187, N.188, I.189, T.191, P.192, L.193, W.194 Ligands: 9MB.12 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:P.186 Hydrogen bonds: C:G.18, C:G.20, C:R.21, C:I.23, C:K.43, C:K.43, C:D.44, C:D.64, C:V.65, C:N.91, C:K.160, C:I.189, C:I.189, C:T.191, C:L.193 Water bridges: C:G.24, C:N.91 Salt bridges: C:R.21 pi-Cation interactions: C:K.43 NAD.13: 31 residues within 4Å: Chain D: G.18, G.20, R.21, G.22, I.23, G.24, D.42, K.43, D.44, C.63, D.64, V.65, T.66, N.91, A.92, G.93, L.115, I.141, S.142, S.143, Y.156, K.160, P.186, G.187, N.188, I.189, T.191, P.192, L.193, W.194 Ligands: 9MB.16 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:P.186 Hydrogen bonds: D:G.18, D:G.20, D:R.21, D:I.23, D:K.43, D:K.43, D:D.44, D:D.64, D:V.65, D:N.91, D:K.160, D:I.189, D:I.189, D:T.191, D:L.193 Water bridges: D:G.24, D:N.91 Salt bridges: D:R.21 pi-Cation interactions: D:K.43

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

NA.2: 5 residues within 4Å: Chain A: E.52, L.55, P.56, G.57, A.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.55, A:A.58 NA.6: 5 residues within 4Å: Chain B: E.52, L.55, P.56, G.57, A.58 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.52, B:A.58 NA.10: 5 residues within 4Å: Chain C: E.52, L.55, P.56, G.57, A.58 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.52, C:A.58 NA.14: 5 residues within 4Å: Chain D: E.52, L.55, P.56, G.57, A.58 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.55, D:A.58

4 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.3: 6 residues within 4Å: Chain A: G.22, W.190, T.191, P.192, E.195, P.223 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:G.22, A:G.22, A:W.190, A:E.195 Water bridges: D:D.269 BGC.7: 6 residues within 4Å: Chain B: G.22, W.190, T.191, P.192, E.195, P.223 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.22, B:G.22, B:W.190, B:E.195 Water bridges: C:D.269 BGC.11: 6 residues within 4Å: Chain C: G.22, W.190, T.191, P.192, E.195, P.223 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.22, C:G.22, C:W.190, C:E.195 Water bridges: B:D.269 BGC.15: 6 residues within 4Å: Chain D: G.22, W.190, T.191, P.192, E.195, P.223 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:G.22, D:G.22, D:W.190, D:E.195 Water bridges: A:D.269

4 x 9MB: 2-fluoranyl-3-[6-(4-fluoranyl-3-oxidanyl-phenoxy)pyridin-2-yl]phenol(Non-covalent)

9MB.4: 17 residues within 4Å: Chain A: H.95, P.98, S.143, L.144, V.145, Q.150, A.151, Q.152, A.153, Y.156, P.186, G.187, N.188, W.194, L.197 Chain D: Y.255 Ligands: NAD.1 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:Q.150, A:W.194, A:L.197, A:L.197, D:Y.255 Hydrogen bonds: A:S.143, A:S.143, A:Q.150, A:A.151, A:Y.156 Water bridges: A:Q.99 pi-Stacking: A:H.95 9MB.8: 17 residues within 4Å: Chain B: H.95, P.98, S.143, L.144, V.145, Q.150, A.151, Q.152, A.153, Y.156, P.186, G.187, N.188, W.194, L.197 Chain C: Y.255 Ligands: NAD.5 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Q.150, B:W.194, B:L.197, B:L.197, C:Y.255 Hydrogen bonds: B:S.143, B:S.143, B:Q.150, B:A.151, B:Y.156 Water bridges: B:Q.99 pi-Stacking: B:H.95 9MB.12: 17 residues within 4Å: Chain B: Y.255 Chain C: H.95, P.98, S.143, L.144, V.145, Q.150, A.151, Q.152, A.153, Y.156, P.186, G.187, N.188, W.194, L.197 Ligands: NAD.9 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:Q.150, C:W.194, C:L.197, C:L.197, B:Y.255 Hydrogen bonds: C:S.143, C:S.143, C:Q.150, C:A.151, C:Y.156 Water bridges: C:Q.99 pi-Stacking: C:H.95 9MB.16: 17 residues within 4Å: Chain A: Y.255 Chain D: H.95, P.98, S.143, L.144, V.145, Q.150, A.151, Q.152, A.153, Y.156, P.186, G.187, N.188, W.194, L.197 Ligands: NAD.13 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:Q.150, D:W.194, D:L.197, D:L.197, A:Y.255 Hydrogen bonds: D:S.143, D:S.143, D:Q.150, D:A.151, D:Y.156 Water bridges: D:Q.99 pi-Stacking: D:H.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Braun, F. et al., Structure-based design and profiling of novel 17 beta-HSD14 inhibitors. Eur J Med Chem (2018)

Release Date

2018-06-06

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

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