SMTL ID : 6gtu.1

17beta-hydroxysteroid dehydrogenase 14 variant T205 in complex with fragment J6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 28 residues within 4Å: Chain A: G.18, G.20, R.21, G.22, I.23, D.42, K.43, D.44, C.63, D.64, V.65, 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 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.23, A:P.186 Hydrogen bonds: A:G.18, A:G.20, A:R.21, A:I.23, A:K.43, A:D.64, A:V.65, A:N.91, A:Y.156, A:K.160, A:I.189, A:I.189, A:L.193 Water bridges: A:G.24, A:N.91 Salt bridges: A:R.21 NAD.5: 28 residues within 4Å: Chain B: G.18, G.20, R.21, G.22, I.23, D.42, K.43, D.44, C.63, D.64, V.65, 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 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.23, B:P.186 Hydrogen bonds: B:G.18, B:G.20, B:R.21, B:I.23, B:K.43, B:D.64, B:V.65, B:N.91, B:Y.156, B:K.160, B:I.189, B:I.189, B:L.193 Water bridges: B:G.24, B:N.91 Salt bridges: B:R.21 NAD.9: 28 residues within 4Å: Chain C: G.18, G.20, R.21, G.22, I.23, D.42, K.43, D.44, C.63, D.64, V.65, 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 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:I.23, C:P.186 Hydrogen bonds: C:G.18, C:G.20, C:R.21, C:I.23, C:K.43, 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 NAD.13: 28 residues within 4Å: Chain D: G.18, G.20, R.21, G.22, I.23, D.42, K.43, D.44, C.63, D.64, V.65, 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 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:I.23, D:P.186 Hydrogen bonds: D:G.18, D:G.20, D:R.21, D:I.23, D:K.43, 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

4 x 45N: N-(1,3-benzodioxol-5-ylmethyl)cyclopentanamine(Non-covalent)

45N.2: 11 residues within 4Å: Chain A: Q.150, A.151, N.188, W.194, E.210, G.211, K.258, S.260 Chain B: L.172 Chain D: Y.255 Ligands: CL.4 6 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: A:A.151, D:Y.255, B:L.172 Hydrogen bonds: A:Q.150, A:N.188, D:Y.255 45N.6: 11 residues within 4Å: Chain A: L.172 Chain B: Q.150, A.151, N.188, W.194, E.210, G.211, K.258, S.260 Chain C: Y.255 Ligands: CL.8 6 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: C:Y.255, A:L.172, B:A.151 Hydrogen bonds: C:Y.255, B:Q.150, B:N.188 45N.10: 11 residues within 4Å: Chain B: Y.255 Chain C: Q.150, A.151, N.188, W.194, E.210, G.211, K.258, S.260 Chain D: L.172 Ligands: CL.12 6 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: B:Y.255, D:L.172, C:A.151 Hydrogen bonds: B:Y.255, C:Q.150, C:N.188 45N.14: 11 residues within 4Å: Chain A: Y.255 Chain C: L.172 Chain D: Q.150, A.151, N.188, W.194, E.210, G.211, K.258, S.260 Ligands: CL.16 6 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: D:A.151, A:Y.255, C:L.172 Hydrogen bonds: D:Q.150, D:N.188, A:Y.255

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

PGE.3: 5 residues within 4Å: Chain A: W.190, R.205, I.208 Chain D: P.268, D.269 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.195 PGE.7: 5 residues within 4Å: Chain B: W.190, R.205, I.208 Chain C: P.268, D.269 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.195 PGE.11: 5 residues within 4Å: Chain B: P.268, D.269 Chain C: W.190, R.205, I.208 No protein-ligand interaction detected (PLIP) PGE.15: 5 residues within 4Å: Chain A: P.268, D.269 Chain D: W.190, R.205, I.208 No protein-ligand interaction detected (PLIP)

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 5 residues within 4Å: Chain A: Q.150, A.151 Chain D: G.254, Y.255 Ligands: 45N.2 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: Q.150, A.151 Chain C: G.254, Y.255 Ligands: 45N.6 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain B: G.254, Y.255 Chain C: Q.150, A.151 Ligands: 45N.10 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain A: G.254, Y.255 Chain D: Q.150, A.151 Ligands: 45N.14 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bertoletti, N. et al., X-ray Crystallographic Fragment screening and Hit Optimization. To Be Published

Release Date

2019-07-03

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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