Structure of PDB 5vp5 Chain A Binding Site BS01

Receptor Information

>5vp5 Chain A (length=411) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

QPETLRRYRPGDPPLAGSLLIGGSGRVAEPLRTALADDYNLVSNNIGGRW
ADSFGGVVFDATGITEAEGLKELYTFFTPLLRNLAPCARVVVVGTTPAEA
GSVHAQVVQRALEGFTRSLGKELRRGATVSLVYLSADAKPGATGLESTMR
FILSAKSAYVDGQVFRVGAADSTPPADWDKPLDGKVAVVTGAARGIGATI
AEVFARDGATVVAIDVDGAAEDLKRVADKVGGTALTLDVTADDAVDKITA
HVTEHHGGKVDILVNNAGITRDKLLANMDEKRWDAVIAVNLLAPQRLTEG
LVGNGTIGEGGRVIGLSSMAGIAGNRGQTNYATTKAGMIGLAEALAPVLA
DKGITINAVAPGFIETRRLNSLFQGGQPVDVAELIAYFASPASNAVTGNT
IRVCGQAMLGA

Ligand information

• Ligand ID: NAD
• InChI: InChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
• InChIKey: BAWFJGJZGIEFAR-NNYOXOHSSA-N
• SMILES:
  CACTVS 3.341: NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
  OpenEye OEToolkits 1.5.0: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
  CACTVS 3.341: NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
  OpenEye OEToolkits 1.5.0: c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
• Formula: C21 H27 N7 O14 P2
• Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
• ChEMBL: CHEMBL1234613
• DrugBank: DB14128
• PDB chain: 5vp5 Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5vp5 Crystal structure of a 3-oxoacyl-acyl-carrier protein reductase FabG4 from Mycobacterium smegmatis bound to NAD
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): G216 R219 I221 D240 V241 D263 V264 N291 A292 I294 S343 Y356 K360 P386
• Binding residue (residue number reindexed from 1): G191 R194 I196 D215 V216 D238 V239 N266 A267 I269 S318 Y331 K335 P361
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): S343 Y356 K360
• Catalytic site (residue number reindexed from 1): S318 Y331 K335
• Enzyme Commision number: 1.1.1.100: 3-oxoacyl-[acyl-carrier-protein] reductase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0016491 oxidoreductase activity
• GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

Biological Process

• GO:0030497 fatty acid elongation

External links

• PDB: RCSB:5vp5, PDBe:5vp5, PDBj:5vp5
• PDBsum: 5vp5
• PubMed: 38656226
• UniProt: A0QPE7