SMTL ID : 9iuo.2 (1 other biounit)

Human MTHFD1 in complex with compound 16d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 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: 14 residues within 4Å: Chain A: Y.51, V.54, K.55, V.98, Q.99, L.100, D.124, L.126, I.237, P.271, G.272, G.275, P.276, V.279 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.51, A:I.237, A:V.279 Hydrogen bonds: A:K.55, A:V.98, A:Q.99, A:L.100, A:L.100, A:L.100, A:G.272 Water bridges: A:C.146, A:G.273, A:G.275 Salt bridges: A:D.124 pi-Stacking: A:Y.51 pi-Cation interactions: A:K.55 01.3: 16 residues within 4Å: Chain B: Y.51, V.54, K.55, L.97, V.98, Q.99, L.100, D.124, L.126, I.175, I.237, P.271, G.272, G.275, P.276, V.279 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.51, B:Y.51, B:V.279 Hydrogen bonds: B:K.55, B:V.98, B:Q.99, B:L.100, B:L.100, B:L.100, B:G.272, B:G.275 Water bridges: B:R.16, B:G.273, B:G.275 Salt bridges: B:D.124

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

NAP.2: 18 residues within 4Å: Chain A: V.170, G.171, R.172, S.173, V.176, H.195, S.196, L.201, A.214, T.215, G.216, Q.217, M.220, C.235, G.236, I.237, N.238, D.254 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.172, A:S.173, A:S.196, A:S.196, A:S.196, A:G.216, A:Q.217, A:I.237, A:N.238 Water bridges: A:R.172, A:R.172, A:K.197, A:T.215 Salt bridges: A:R.172 NAP.4: 18 residues within 4Å: Chain B: V.170, G.171, R.172, S.173, I.175, H.195, S.196, L.201, A.214, T.215, G.216, Q.217, M.220, C.235, G.236, I.237, N.238, D.254 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.172, B:S.173, B:S.196, B:S.196, B:S.196, B:G.216, B:Q.217, B:I.237, B:D.254 Salt bridges: B:R.172

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

C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed

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