SMTL ID : 7km8.3 (2 other biounits)

Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001914, orthorhombic crystal from

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 28 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: WPD.2 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: 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:R.77, A:R.77, A:Q.78, A:Q.78, A:G.109, A:G.110, A:A.111, A:Q.112, A:I.113 Water bridges: A:R.26, A:R.77, A:R.77, A:Q.112, A:Q.112, A:Q.112, A:Q.112 Salt bridges: A:R.54, A:R.55 pi-Cation interactions: A:R.77, A:R.77 NAP.7: 28 residues within 4Å: Chain B: 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: WPD.8 34 PLIP interactions: 34 interactions with chain B Hydrophobic interactions: B:T.56 Hydrogen bonds: B:A.17, B:I.24, B:R.26, B:G.28, B:G.28, B:G.53, B:R.54, B:R.54, B:R.55, B:T.56, B:T.56, B:S.59, B:T.76, B:T.76, B:R.77, B:R.77, B:Q.78, B:Q.78, B:G.109, B:G.110, B:A.111, B:Q.112, B:I.113, B:Y.114 Water bridges: B:G.25, B:R.55, B:R.55, B:Q.112, B:Q.112 Salt bridges: B:R.54, B:R.55 pi-Cation interactions: B:R.77, B:R.77

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

WPD.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, R.70, I.108, Y.114, T.127 Chain B: R.33, S.161 Ligands: NAP.1 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.30, A:L.38, A:L.38, A:P.61, A:H.64, B:R.33 Hydrogen bonds: A:I.15, A:Y.114, A:T.127, A:T.127 Salt bridges: A:D.37, A:K.42, A:R.70 WPD.8: 19 residues within 4Å: Chain A: R.33, S.161 Chain B: I.15, W.16, A.17, I.30, D.37, L.38, F.41, K.42, L.60, P.61, H.64, L.67, R.70, I.108, Y.114, T.127 Ligands: NAP.7 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.30, B:P.61, B:H.64, A:R.33 Hydrogen bonds: B:I.15, B:T.127, B:T.127 Salt bridges: B:D.37, B:R.70

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

CL.3: 4 residues within 4Å: Chain A: R.33, L.34, P.35, L.38 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain B: R.33, L.34, L.38 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: R.33 Chain B: G.29, I.30, R.33 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: G.29, I.30, R.33 Chain B: R.33 Ligand excluded by PLIP

Links

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Citation

Abendroth, J. et al., Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001914, orthorhombic crystal form. to be published

Release Date

2021-07-07

Peptides

Dihydrofolate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrofolate reductase

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