SMTL ID : 6buv.1

Structure of Mycobacterium tuberculosis NadD in complex with inhibitor [(1~{R},2~{R},5~{S})-5-methyl-2-propan-2-yl-cyclohexyl] 2-[3-methyl-2-(phenoxymethyl)benzimidazol-1-yl]ethanoate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

1 x NA: SODIUM ION(Non-functional Binders)

NA.1: 5 residues within 4Å: Chain A: R.129, L.152, D.155, L.157, T.158 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.129, A:D.155, A:D.155, A:T.158

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

CL.2: 3 residues within 4Å: Chain A: Y.193, K.196, R.197 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: R.5, H.98, P.99, D.100, S.101 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: Y.86, K.88, Q.119, G.120 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain B: Y.193, K.196, R.197 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain B: H.18, H.21, R.135, S.168, S.169 Ligand excluded by PLIP

1 x E9A: 1-methyl-3-(2-{[(1R,2R,5S)-5-methyl-2-(propan-2-yl)cyclohexyl]oxy}-2-oxoethyl)-2-(phenoxymethyl)-1H-1,3-benzimidazol-3-ium(Non-covalent)

E9A.5: 14 residues within 4Å: Chain B: A.109, D.110, A.113, S.114, M.116, S.117, W.118, W.121, I.145, L.148, L.149, L.152, L.157, L.159 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.109, B:I.145, B:L.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osterman, A.L. et al., Novel Antimycobacterial Compounds Suppress NAD Biogenesis by Targeting a Unique Pocket of NaMN Adenylyltransferase. Acs Chem.Biol. (2019)

Release Date

2018-12-12

Peptides

nicotinate mononucleotide adenylyltransferase NadD: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

nicotinate mononucleotide adenylyltransferase NadD

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