SMTL ID : 6p4v.1

1.65 Angstrom ternary complex of Deoxyhypusine synthase with cofactor NAD and spermidine mimic inhibitor GC7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 31 residues within 4Å: Chain A: T.107, S.108, N.109, L.110, S.112, T.134, A.135, G.136, E.139, E.140, I.169, D.241, G.242, G.285, G.286, I.309, N.310, T.311, A.312, A.344, D.345, A.346 Chain B: G.287, V.288, H.291, D.316, S.318, D.319, S.320 Ligands: NAD.4, GC7.5 24 PLIP interactions: 18 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:T.107, A:S.108, A:S.108, A:N.109, A:N.109, A:S.112, A:T.134, A:T.134, A:A.135, A:G.136, A:E.140, A:G.286, A:T.311, A:D.345, A:A.346, B:G.287, B:D.319, B:S.320, B:S.320, B:S.320, B:S.320 Water bridges: A:N.109, A:N.109, A:G.286 NAD.4: 31 residues within 4Å: Chain A: G.287, V.288, H.291, D.316, S.318, D.319, S.320 Chain B: T.107, S.108, N.109, L.110, S.112, T.134, A.135, G.136, E.139, E.140, I.169, D.241, G.242, G.285, G.286, I.309, N.310, T.311, A.312, A.344, D.345, A.346 Ligands: NAD.1, GC7.2 27 PLIP interactions: 19 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:T.107, B:S.108, B:S.108, B:N.109, B:S.112, B:T.134, B:T.134, B:A.135, B:G.136, B:E.140, B:G.286, B:T.311, B:T.311, B:D.345, B:D.345, B:A.346, A:G.287, A:D.319, A:S.320, A:S.320, A:S.320, A:S.320 Water bridges: B:N.109, B:N.109, B:G.286, A:D.316, A:S.318 NAD.6: 31 residues within 4Å: Chain C: T.107, S.108, N.109, L.110, S.112, T.134, A.135, G.136, E.139, E.140, I.169, D.241, G.242, G.285, G.286, I.309, N.310, T.311, A.312, A.344, D.345, A.346 Chain D: G.287, V.288, H.291, D.316, S.318, D.319, S.320 Ligands: NAD.9, GC7.10 23 PLIP interactions: 6 interactions with chain D, 17 interactions with chain C Hydrogen bonds: D:G.287, D:D.319, D:S.320, D:S.320, D:S.320, D:S.320, C:S.108, C:S.108, C:N.109, C:N.109, C:S.112, C:T.134, C:A.135, C:G.136, C:E.140, C:D.241, C:G.286, C:T.311, C:T.311, C:A.346 Water bridges: C:N.109, C:N.109, C:G.286 NAD.9: 31 residues within 4Å: Chain C: G.287, V.288, H.291, D.316, S.318, D.319, S.320 Chain D: T.107, S.108, N.109, L.110, S.112, T.134, A.135, G.136, E.139, E.140, I.169, D.241, G.242, G.285, G.286, I.309, N.310, T.311, A.312, A.344, D.345, A.346 Ligands: NAD.6, GC7.7 24 PLIP interactions: 17 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:S.108, D:S.108, D:N.109, D:S.112, D:T.134, D:A.135, D:G.136, D:E.140, D:D.241, D:G.286, D:T.311, D:D.345, D:A.346, C:G.287, C:D.319, C:S.320, C:S.320, C:S.320, C:S.320 Water bridges: D:N.109, D:N.109, D:G.286, D:T.311, C:D.316

4 x GC7: 1-GUANIDINIUM-7-AMINOHEPTANE(Non-covalent)

GC7.2: 16 residues within 4Å: Chain A: H.291, N.295, L.298, G.317, S.318, D.319, A.322, E.326, W.330, K.332 Chain B: N.109, I.169, G.170, S.243, D.246 Ligands: NAD.4 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:W.330, A:W.330, A:W.330 Hydrogen bonds: A:N.295, A:G.317, A:G.317, B:G.170, B:D.246 Salt bridges: A:D.319, A:E.326 Water bridges: B:N.109, B:D.246 GC7.5: 15 residues within 4Å: Chain A: N.109, I.169, G.170, S.243, D.246 Chain B: H.291, N.295, L.298, G.317, S.318, D.319, E.326, W.330, K.332 Ligands: NAD.1 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.330, B:W.330, B:W.330 Hydrogen bonds: B:N.295, B:G.317, B:G.317, A:G.170, A:D.246 Salt bridges: B:D.319, B:E.326 Water bridges: A:N.109 GC7.7: 16 residues within 4Å: Chain C: H.291, N.295, L.298, G.317, S.318, D.319, A.322, E.326, W.330, K.332 Chain D: N.109, I.169, G.170, S.243, D.246 Ligands: NAD.9 12 PLIP interactions: 3 interactions with chain D, 9 interactions with chain C Hydrogen bonds: D:G.170, D:D.246, C:N.295, C:G.317, C:G.317 Water bridges: D:N.109, C:E.326 Hydrophobic interactions: C:W.330, C:W.330, C:W.330 Salt bridges: C:D.319, C:E.326 GC7.10: 15 residues within 4Å: Chain C: N.109, I.169, G.170, S.243, D.246 Chain D: H.291, N.295, L.298, G.317, S.318, D.319, E.326, W.330, K.332 Ligands: NAD.6 13 PLIP interactions: 9 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:W.330, D:W.330, D:W.330 Hydrogen bonds: D:N.295, D:G.317, D:G.317, C:G.170, C:D.246 Water bridges: D:E.326, C:N.109, C:D.246 Salt bridges: D:D.319, D:E.326

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 3 residues within 4Å: Chain A: R.41, G.42, V.43 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.43 MPD.8: 3 residues within 4Å: Chain C: R.41, G.42, V.43 1 PLIP interactions: 1 interactions with chain C Water bridges: C:V.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanaka, Y. et al., Discovery of Novel Allosteric Inhibitors of Deoxyhypusine Synthase. J.Med.Chem. (2020)

Release Date

2020-04-01

Peptides

Deoxyhypusine synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Deoxyhypusine synthase

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