SMTL ID : 9is9.1

human MTHFD2 in complex with LY374571

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-dimer

Ligands

2 x 9L9: (2S)-2-[[4-[[2,4-bis(azanyl)-6-oxidanylidene-1H-pyrimidin-5-yl]carbamoylamino]phenyl]carbonylamino]pentanedioic acid(Non-covalent)

9L9.1: 19 residues within 4Å: Chain A: S.52, Y.53, N.56, K.57, L.99, V.100, Q.101, L.102, D.124, F.126, I.245, L.258, P.278, G.279, G.282, P.283, T.285, V.286 Ligands: NAD.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.53, A:Y.53, A:I.245, A:T.285, A:V.286 Hydrogen bonds: A:S.52, A:N.56, A:K.57, A:V.100, A:Q.101, A:L.102, A:L.102, A:G.279, A:G.282 Water bridges: A:K.57, A:A.144, A:T.145, A:G.280 Salt bridges: A:D.124 pi-Stacking: A:Y.53 pi-Cation interactions: A:K.57 9L9.3: 17 residues within 4Å: Chain B: Y.53, N.56, K.57, L.99, V.100, Q.101, L.102, D.124, F.126, I.245, P.278, G.279, G.282, P.283, T.285, V.286 Ligands: NAD.4 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Y.53, B:I.245, B:T.285, B:V.286 Hydrogen bonds: B:S.52, B:N.56, B:K.57, B:V.100, B:Q.101, B:L.102, B:L.102, B:G.279, B:G.282 Water bridges: B:K.57, B:V.100, B:A.144, B:G.280 Salt bridges: B:D.124 pi-Stacking: B:Y.53 pi-Cation interactions: B:K.57

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 21 residues within 4Å: Chain A: T.145, G.169, R.170, S.171, V.174, S.200, H.201, R.202, A.222, A.223, G.224, I.225, V.243, G.244, I.245, N.246, V.281, G.282, T.285 Ligands: 9L9.1, PO4.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.170, A:S.171, A:S.171, A:S.171, A:R.202, A:R.202, A:I.245, A:N.246, A:V.281 Water bridges: A:G.175 NAD.4: 19 residues within 4Å: Chain B: T.145, G.169, R.170, S.171, V.174, H.201, R.202, A.222, A.223, G.224, L.228, V.243, G.244, I.245, V.281, G.282, T.285 Ligands: 9L9.3, PO4.6 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:T.145 Hydrogen bonds: B:R.170, B:S.171, B:R.202, B:R.202, B:I.245, B:V.281, B:T.285 Water bridges: B:S.171, B:S.171

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

PO4.5: 6 residues within 4Å: Chain A: R.170, S.171, R.202 Chain B: D.185, H.188 Ligands: NAD.2 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:R.170 Salt bridges: A:R.170, A:R.202, B:H.188 PO4.6: 5 residues within 4Å: Chain A: D.185, H.188 Chain B: R.170, R.202 Ligands: NAD.4 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.185, A:D.185, A:D.185 Salt bridges: A:H.188, B:R.170, B:R.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, H.H. et al., Development of Potent and Selective Inhibitors of Methylenetetrahydrofolate Dehydrogenase 2 for Targeting Acute Myeloid Leukemia: SAR, Structural Insights, and Biological Characterization. J.Med.Chem. (2024)

Release Date

2025-01-01

Peptides

Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial

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