SMTL ID : 7k6a.1

Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001575

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

NAP.1: 30 residues within 4Å: Chain A: W.16, A.17, I.24, G.25, R.26, G.28, G.29, I.30, G.53, R.54, R.55, T.56, S.59, V.75, T.76, R.77, Q.78, G.90, I.108, G.109, G.110, A.111, Q.112, I.113, Y.114, L.116, A.140 Ligands: VYG.2, EDO.5, EDO.6 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:I.30, A:T.56 Hydrogen bonds: A:A.17, A:I.24, A:R.26, A:G.28, A:G.28, A:G.53, A:R.54, A:R.54, A:R.55, A:T.56, A:S.59, A:T.76, A:T.76, A:R.77, A:R.77, A:R.77, A:Q.78, A:Q.78, A:G.110, A:A.111, A:Q.112, A:Q.112, A:I.113 Water bridges: A:Q.112 Salt bridges: A:R.54, A:R.55 pi-Cation interactions: A:R.77

1 x VYG: 6-ethyl-5-[3-({3-[4-(trifluoromethyl)piperidin-1-yl]pyridin-2-yl}oxy)propoxy]pyrimidine-2,4-diamine(Non-covalent)

VYG.2: 19 residues within 4Å: Chain A: I.15, W.16, A.17, I.30, D.37, L.38, F.41, K.42, L.60, P.61, H.64, L.67, P.68, R.70, I.108, Y.114, T.127 Ligands: NAP.1, CL.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.30, A:L.38, A:P.61, A:H.64, A:L.67 Hydrogen bonds: A:I.15, A:Y.114, A:T.127, A:T.127 Water bridges: A:T.127 Salt bridges: A:D.37

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

CL.3: 4 residues within 4Å: Chain A: K.42, M.46, R.70 Ligands: VYG.2 Ligand excluded by PLIP

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

EDO.4: 4 residues within 4Å: Chain A: A.83, A.86, Q.87, V.88 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.83, A:A.83, A:V.88, A:V.88 EDO.5: 9 residues within 4Å: Chain A: G.25, R.26, D.27, G.28, R.55, E.138, A.140 Ligands: NAP.1, EDO.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.26, A:G.28, A:R.55 Water bridges: A:D.27, A:R.55, A:R.55 EDO.6: 7 residues within 4Å: Chain A: R.55, Q.112, E.138, D.139, A.140 Ligands: NAP.1, EDO.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.112, A:D.139 Water bridges: A:R.55, A:R.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001575. to be published

Release Date

2021-03-17

Peptides

Dihydrofolate reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydrofolate reductase

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