SMTL ID : 9isc.1

Human MTHFD2 in complex with compound 16a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.54 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 19 residues within 4Å: Chain A: T.145, G.169, R.170, S.171, V.174, H.201, R.202, A.222, A.223, G.224, I.225, V.243, G.244, I.245, V.281, G.282, T.285 Ligands: 01.2, PO4.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.170, A:R.170, A:S.171, A:S.171, A:R.202, A:A.223, A:I.245, A:V.281, A:T.285 Water bridges: A:S.171, A:G.175 NAD.5: 18 residues within 4Å: Chain B: Y.53, G.169, R.170, S.171, V.174, S.200, H.201, R.202, K.206, A.222, A.223, G.224, I.225, V.243, G.244, I.245 Ligands: PO4.4, 01.6 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.170, B:S.171, B:R.202, B:R.202, B:R.202, B:K.206, B:K.206, B:I.245, B:N.246 Water bridges: B:Q.101

2 x 01: (2~{S})-2-[[4-[[2,4-bis(azanyl)-6-oxidanylidene-1~{H}-pyrimidin-5-yl]carbamoylamino]phenyl]carbonylamino]-4-(1~{H}-1,2,3,4-tetrazol-5-yl)butanoic acid

01.2: 20 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, R.247, L.258, P.278, G.279, G.282, P.283, T.285, V.286 Ligands: NAD.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: 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:R.247, A:G.279, A:G.282 Water bridges: A:A.144, A:G.280, A:G.280 Salt bridges: A:D.124 pi-Stacking: A:Y.53 pi-Cation interactions: A:K.57 01.6: 18 residues within 4Å: Chain B: R.12, 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 Ligands: NAD.5 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.53, B:P.278, B:T.285 Hydrogen bonds: B:R.12, 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:A.144, B:T.145 Salt bridges: B:D.124 pi-Stacking: B:Y.53 pi-Cation interactions: B:K.57

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

PO4.3: 6 residues within 4Å: Chain A: R.170, S.171, R.202 Chain B: D.185, H.188 Ligands: NAD.1 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.185, B:D.185, B:D.185 Water bridges: B:D.185 Salt bridges: B:H.188, A:R.170, A:R.202 PO4.4: 5 residues within 4Å: Chain A: D.185, H.188 Chain B: R.170, R.202 Ligands: NAD.5 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.170, B:R.202, A:H.188

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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