SMTL ID : 5cr5.1

X-RAY CRYSTAL STRUCTURE AT 1.61A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A BIPHENYL PYRROLIDINE ETHER COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 15 residues within 4Å: Chain A: R.103, R.196, K.206, Y.211, E.241, T.244, M.245, N.246, L.270, G.272, V.273, V.274, G.316, T.317 Ligands: EL1.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:K.206, A:L.270 Hydrogen bonds: A:K.206, A:Y.211, A:V.273, A:V.274, A:T.317, A:T.317 Water bridges: A:R.103, A:R.103, A:R.103, A:R.103, A:R.275 Salt bridges: A:R.103, A:K.206 PLP.9: 15 residues within 4Å: Chain B: R.103, R.196, K.206, Y.211, E.241, T.244, M.245, N.246, L.270, G.272, V.273, V.274, G.316, T.317 Ligands: EL1.10 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:K.206, B:L.270 Hydrogen bonds: B:Y.211, B:Y.211, B:V.273, B:V.274, B:T.317, B:T.317 Water bridges: B:R.103, B:R.103, B:R.103, B:R.103, B:R.275 Salt bridges: B:R.103, B:K.206

2 x EL1: 3-({(3R)-1-[(5-bromothiophen-2-yl)carbonyl]pyrrolidin-3-yl}oxy)-N-methyl-2'-[(methylsulfonyl)amino]biphenyl-4-carboxamide(Non-covalent)

EL1.2: 19 residues within 4Å: Chain A: F.34, F.79, R.147, Y.177, V.186, K.206, Q.228, V.242, G.243, T.244, M.245, G.314, G.316, T.317, A.318, C.322, V.324 Chain B: Y.74 Ligands: PLP.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.34, A:F.34, A:F.79, A:V.186, A:Q.228, A:A.318 Hydrogen bonds: A:T.244, A:T.244, A:T.244, A:T.317, A:A.318 Water bridges: A:F.34 EL1.10: 19 residues within 4Å: Chain A: Y.74 Chain B: F.34, F.79, R.147, Y.177, V.186, K.206, Q.228, V.242, G.243, T.244, M.245, G.314, G.316, T.317, A.318, C.322, V.324 Ligands: PLP.9 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.34, B:F.34, B:F.79, B:V.186, B:Q.228, B:A.318, A:Y.74 Hydrogen bonds: B:T.244, B:T.244, B:T.317, B:A.318

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: K.83, A.318, Q.320 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: K.83, Q.320 Ligand excluded by PLIP

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: Y.250, E.287, E.344, L.345, R.348 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.250, A:E.287, A:R.348 Water bridges: A:Y.250, A:R.310 EDO.5: 5 residues within 4Å: Chain A: V.199, Y.233, Q.238, N.266, T.294 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.238, A:N.266, A:N.266 Water bridges: A:Y.233 EDO.6: 4 residues within 4Å: Chain A: I.195, Y.233, G.234 Chain B: W.198 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.234 Water bridges: A:P.192, A:P.192, A:Y.233 EDO.7: 4 residues within 4Å: Chain A: E.46, L.63, T.64, L.166 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.62, A:T.64, A:T.64 Water bridges: A:E.46, A:E.46, A:T.64 EDO.8: 3 residues within 4Å: Chain A: P.264, L.265, N.266 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.265, A:L.265 EDO.12: 5 residues within 4Å: Chain B: Y.250, R.310, E.344, L.345, R.348 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.250, B:R.310, B:E.344, B:R.348 Water bridges: B:R.310

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.13: 5 residues within 4Å: Chain B: E.46, R.56, L.63, T.64, L.166 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.64 Water bridges: B:T.64 Salt bridges: B:E.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, H. et al., Discovery, SAR, and X-ray Binding Mode Study of BCATm Inhibitors from a Novel DNA-Encoded Library. Acs Med.Chem.Lett. (2015)

Release Date

2015-08-12

Peptides

Branched-chain-amino-acid aminotransferase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Branched-chain-amino-acid aminotransferase, mitochondrial

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