SMTL ID : 8cqa.1

Mycobacterium tuberculosis dihydrofolate reductase in complex with N-(4-(2,6-diamino-5-(cyclopropylethynyl)pyrimidin-4-yl)phenyl)acetamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x VF6: ~{N}-[4-[2,6-bis(azanyl)-5-(2-cyclopropylethyl)pyrimidin-4-yl]phenyl]ethanamide(Non-covalent)

VF6.1: 13 residues within 4Å: Chain A: I.5, W.6, A.7, R.23, D.27, Q.28, F.31, T.46, L.50, I.94, Y.100, T.113 Ligands: NDP.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:R.23, A:Q.28, A:F.31, A:F.31, A:T.46, A:L.50, A:I.94 Hydrogen bonds: A:W.6, A:R.23, A:I.94, A:Y.100, A:T.113 Water bridges: A:T.113, A:T.113 Salt bridges: A:D.27 pi-Stacking: A:F.31 VF6.8: 16 residues within 4Å: Chain B: I.5, W.6, A.7, I.20, R.23, L.24, D.27, Q.28, F.31, T.46, L.50, I.94, Y.100, T.113 Ligands: MES.9, NDP.10 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.20, B:Q.28, B:F.31, B:F.31, B:T.46, B:L.50, B:I.94 Hydrogen bonds: B:W.6, B:Y.100, B:Y.100 Salt bridges: B:D.27 pi-Stacking: B:F.31

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.2: 27 residues within 4Å: Chain A: W.6, A.7, I.14, G.15, G.18, D.19, I.20, W.22, G.43, R.44, R.45, T.46, S.49, L.65, S.66, R.67, Q.68, G.80, I.94, G.95, G.96, G.97, Q.98, V.99, Y.100, L.102 Ligands: VF6.1 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:A.7, A:I.14, A:G.43, A:R.44, A:R.45, A:R.45, A:T.46, A:S.49, A:S.49, A:R.67, A:R.67, A:Q.68, A:G.95, A:G.96, A:G.97, A:Q.98, A:V.99 Water bridges: A:G.18 Salt bridges: A:R.44 pi-Cation interactions: A:R.67, A:R.67 NDP.10: 28 residues within 4Å: Chain B: W.6, A.7, I.14, G.15, R.16, G.18, D.19, I.20, W.22, G.43, R.44, R.45, T.46, L.65, S.66, R.67, Q.68, G.80, I.94, G.95, G.96, G.97, Q.98, V.99, Y.100, L.102, A.126 Ligands: VF6.8 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:I.20, B:T.46 Hydrogen bonds: B:A.7, B:A.7, B:R.16, B:G.18, B:G.18, B:R.44, B:R.45, B:T.46, B:T.46, B:R.67, B:R.67, B:R.67, B:G.96, B:G.96, B:G.97, B:Q.98, B:V.99 Water bridges: B:S.49 Salt bridges: B:R.44, B:R.45, B:R.67 pi-Cation interactions: B:R.67, B:R.67

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

CO.3: 4 residues within 4Å: Chain A: I.34, H.38 Chain B: H.157, S.159 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.38, B:H.157, H2O.1 CO.4: 3 residues within 4Å: Chain A: H.157 Chain B: I.34, H.38 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.157, B:H.38

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

SO4.5: 3 residues within 4Å: Chain A: F.31, L.57, R.60 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.60 SO4.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.7: 2 residues within 4Å: Chain A: R.44, R.45 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.44, A:R.45 SO4.11: 2 residues within 4Å: Chain B: R.44, R.45 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.44, B:R.45

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.9: 8 residues within 4Å: Chain B: Q.28, F.31, R.32, L.50, V.54, L.57, R.60 Ligands: VF6.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.28 Salt bridges: B:R.32, B:R.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kirkman, T.J. et al., Expansion of a series of pyrimidine derivatives utilising fragment-based merging leads to increased affinity to Mycobacterium tuberculosis dihydrofolate reductase (unpublished currently). To Be Published

Release Date

2024-03-13

Peptides

Dihydrofolate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrofolate reductase

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