SMTL ID : 5sd8.1

Crystal Structure of Dihydrofolate Reductase from Homo sapiens bound to NADP and SDDC Inhibitor SDDC-1190 (racemic mixture)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

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

NAP.1: 31 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, S.60, 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: HJI.2, I6J.3 29 PLIP interactions: 29 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:K.55, A:K.56, A:R.78, A:S.119, A:S.120, A:T.147, A:T.147 Salt bridges: A:K.55

1 x HJI: (2R)-2-[(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)methyl]-3,3-difluoropropanoic acid(Non-covalent)

HJI.2: 17 residues within 4Å: Chain A: I.8, V.9, A.10, D.22, L.23, E.31, F.32, F.35, S.60, P.62, N.65, L.68, V.116, Y.122, T.137 Ligands: NAP.1, I6J.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.23, A:L.23 Hydrogen bonds: A:V.9, A:V.116, A:Y.122, A:T.137 Salt bridges: A:E.31 Halogen bonds: A:N.65

1 x I6J: (2S)-2-[(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)methyl]-3,3-difluoropropanoic acid(Non-covalent)

I6J.3: 17 residues within 4Å: Chain A: I.8, V.9, A.10, L.23, E.31, F.32, F.35, S.60, I.61, P.62, N.65, L.68, V.116, Y.122, T.137 Ligands: NAP.1, HJI.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.23 Hydrogen bonds: A:I.8, A:V.9, A:N.65, A:Y.122, A:T.137 Salt bridges: A:E.31

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

SO4.4: 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 SO4.5: 3 residues within 4Å: Chain A: R.29, F.32, Q.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.36 Salt bridges: A:R.29

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

CL.6: 4 residues within 4Å: Chain A: M.15, R.138, E.151, I.152 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-1190 (racemic mixture). 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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