SMTL ID : 5sd6.1

Crystal Structure of Dihydrofolate Reductase from Homo sapiens bound to NADP and SDDC Inhibitor SDDC-892

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

1 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 29 residues within 4Å: Chain A: V.9, A.10, I.17, G.18, K.19, G.21, D.22, L.23, W.25, G.54, K.55, K.56, T.57, L.76, S.77, R.78, E.79, R.92, S.93, V.116, G.117, G.118, S.119, S.120, V.121, Y.122, E.124, T.147 Ligands: HXV.2 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:T.57 Hydrogen bonds: A:A.10, A:I.17, A:K.19, A:G.21, A:G.21, A:G.54, A:G.54, A:K.55, A:K.56, A:T.57, A:S.60, A:S.77, A:R.78, A:R.78, A:E.79, A:G.118, A:S.119, A:E.124, A:T.147 Water bridges: A:K.55, A:E.79, A:E.79, A:S.120, A:S.120, A:E.124 Salt bridges: A:K.55

1 x HXV: 6-ethyl-5-(4-{2-[2-(1H-tetrazol-5-yl)ethyl]phenoxy}butoxy)pyrimidine-2,4-diamine(Non-covalent)

HXV.2: 17 residues within 4Å: Chain A: I.8, V.9, A.10, L.23, E.31, F.32, F.35, T.57, I.61, P.62, N.65, L.68, V.116, Y.122, T.137 Ligands: NAP.1, EDO.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.32, A:T.57, A:I.61, A:L.68 Hydrogen bonds: A:I.8, A:Y.122, A:T.137, A:T.137 Water bridges: A:D.22, A:L.28 Salt bridges: A:E.31

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

EDO.3: 4 residues within 4Å: Chain A: P.27, R.29, F.32 Ligands: HXV.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.29 EDO.4: 6 residues within 4Å: Chain A: R.71, I.72, N.73, A.87, H.88, F.89 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.71, A:N.73, A:N.73, A:N.73, A:H.88, A:F.89 Water bridges: A:R.71

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 4 residues within 4Å: Chain A: R.29, F.32, Q.36, K.69 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.36, A:Q.36 Water bridges: A:R.29, A:R.29, A:K.69 Salt bridges: A:R.29, A:K.69 SO4.6: 2 residues within 4Å: Chain A: R.78, R.92 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.78, A:R.92 SO4.7: 2 residues within 4Å: Chain A: R.33, R.37 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.33, A:R.37

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

CL.8: 4 residues within 4Å: Chain A: F.32, F.35, Q.36, R.71 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: M.15, R.138, E.151, I.152 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: T.40, S.42 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mayclin, S.J. et al., Crystal Structure of Dihydrofolate Reductase from Homo sapiens bound to NADP and SDDC Inhibitor SDDC-892. to be published

Release Date

2022-02-09

Peptides

Dihydrofolate reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydrofolate reductase

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