SMTL ID : 6vsf.3 (2 other biounits)

Mycobacterium tuberculosis dihydrofolate reductase in complex with 4-(3,4-dihydro-2H-benzo[b][1,4]dioxepin-7-yl)-4-oxobutanoic acid(fragment 16)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

3 x RKY: 4-(3,4-dihydro-2H-1,5-benzodioxepin-7-yl)-4-oxobutanoic acid(Non-covalent)

RKY.1: 11 residues within 4Å: Chain A: I.22, Q.30, F.33, R.34, T.48, L.52, L.59, R.62, I.96 Ligands: NAP.3, GOL.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Q.30, A:T.48 Water bridges: A:R.34 Salt bridges: A:R.34, A:R.62 pi-Stacking: A:F.33 RKY.6: 11 residues within 4Å: Chain B: I.22, Q.30, F.33, R.34, T.48, L.52, R.62, I.96 Ligands: RKY.7, NAP.9, GOL.10 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Q.30, B:T.48 Salt bridges: B:R.34, B:R.62 pi-Stacking: B:F.33 RKY.7: 10 residues within 4Å: Chain B: D.21, I.22, R.25, Q.30, S.51, L.52, P.53, V.56 Ligands: RKY.6, GOL.10 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.22, B:V.56 Hydrogen bonds: B:Q.30 pi-Cation interactions: B:R.25

2 x CO: COBALT (II) ION(Non-covalent)

CO.2: 4 residues within 4Å: Chain A: I.36, H.40, E.92 Chain B: H.159 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: A:H.40, B:H.159, H2O.1, H2O.2, H2O.2, H2O.10 CO.8: 3 residues within 4Å: Chain B: I.36, H.40, E.92 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.40, H2O.4, H2O.8, H2O.8, H2O.8

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

NAP.3: 28 residues within 4Å: Chain A: W.8, A.9, I.16, G.17, R.18, G.20, D.21, I.22, W.24, G.45, R.46, R.47, T.48, L.67, S.68, R.69, Q.70, G.82, I.96, G.97, G.98, G.99, Q.100, V.101, Y.102, L.104, A.128 Ligands: RKY.1 34 PLIP interactions: 34 interactions with chain A Hydrophobic interactions: A:I.22, A:T.48 Hydrogen bonds: A:A.9, A:I.16, A:R.18, A:G.20, A:G.20, A:G.45, A:R.46, A:R.46, A:R.47, A:T.48, A:T.48, A:R.69, A:R.69, A:R.69, A:Q.70, A:Q.70, A:G.97, A:G.98, A:G.99, A:Q.100, A:Q.100, A:V.101 Water bridges: A:G.17, A:R.47, A:S.51, A:R.69, A:Q.100, A:Y.102 Salt bridges: A:R.46, A:R.47 pi-Cation interactions: A:R.69, A:R.69 NAP.9: 27 residues within 4Å: Chain B: W.8, A.9, I.16, G.17, R.18, G.20, D.21, I.22, G.45, R.46, R.47, T.48, L.67, S.68, R.69, Q.70, G.82, I.96, G.97, G.98, G.99, Q.100, V.101, Y.102, L.104, A.128 Ligands: RKY.6 32 PLIP interactions: 32 interactions with chain B Hydrophobic interactions: B:I.22, B:T.48 Hydrogen bonds: B:A.9, B:R.18, B:G.20, B:G.20, B:G.45, B:R.46, B:R.46, B:R.47, B:R.47, B:T.48, B:T.48, B:R.69, B:R.69, B:R.69, B:Q.70, B:Q.70, B:G.98, B:G.99, B:Q.100, B:V.101, B:Y.102 Water bridges: B:R.18, B:S.51, B:R.69, B:L.84, B:Y.102 Salt bridges: B:R.46, B:R.47 pi-Cation interactions: B:R.69, B:R.69

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: A.9, W.24, R.25, L.26, D.29, Q.30 Ligands: RKY.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.26, A:D.29, A:D.29, A:Q.30 GOL.10: 8 residues within 4Å: Chain B: A.9, W.24, R.25, L.26, D.29, Q.30 Ligands: RKY.6, RKY.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.24, B:L.26, B:Q.30

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 2 residues within 4Å: Chain A: R.46, R.47 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.46, A:R.47 PO4.11: 2 residues within 4Å: Chain B: R.46, R.47 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.46, B:D.50 Salt bridges: B:R.46, B:R.47 PO4.12: 2 residues within 4Å: Chain B: R.34, P.60 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ribeiro, J.A. et al., Using a Fragment-Based Approach to Identify Alternative Chemical Scaffolds Targeting Dihydrofolate Reductase fromMycobacterium tuberculosis. Acs Infect Dis. (2020)

Release Date

2020-07-15

Peptides

Dihydrofolate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrofolate reductase

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