SMTL ID : 9ita.1

Human MTHFD2 in complex with compound 16d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

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

01.1: 18 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 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Y.53, 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:L.102, A:G.279, A:G.282 Water bridges: A:D.124, A:A.144, A:T.145 Salt bridges: A:D.124 pi-Stacking: A:Y.53 pi-Cation interactions: A:K.57 01.4: 18 residues within 4Å: Chain B: S.52, 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.280, G.282, P.283, T.285, V.286 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:Y.53, B:Y.53, B:T.285, B:V.286 Hydrogen bonds: B:S.52, B:S.52, B:N.56, B:K.57, B:V.100, B:Q.101, B:L.102, B:L.102, B:L.102, B:G.279, B:G.280, B:G.282 Water bridges: B:D.124, B:A.144 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: 11 residues within 4Å: Chain A: G.169, R.170, S.171, S.200, H.201, R.202, A.222, A.223, I.225, L.228 Ligands: PO4.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.170, A:S.171, A:R.202, A:R.202, A:R.202 Water bridges: A:S.171 NAD.5: 16 residues within 4Å: Chain B: A.168, G.169, R.170, S.171, S.200, H.201, R.202, A.222, A.223, G.224, I.225, L.228, V.243, G.244, I.245 Ligands: PO4.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.170, B:S.171, B:S.171, B:R.202, B:R.202, B:R.202, B:I.245, B:I.245

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.2 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:H.188, A:R.170, A:R.202 Water bridges: A:K.172 PO4.6: 5 residues within 4Å: Chain A: D.185, H.188 Chain B: R.170, R.202 Ligands: NAD.5 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: 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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