Structure of PDB 6nd3 Chain A Binding Site BS01

Receptor Information
>6nd3 Chain A (length=795) Species: 207559 (Oleidesulfovibrio alaskensis G20) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SGIPDGPTPRHVKLKENFLKQVPSITVQRAVAITKIAKENPGLPKPLLRA
KTFRYCCETAPLVIQDHELIVGSPNGAPRAGAFSPEVAWRWLQDELDTIG
SRPQDPFYISEEDKKVLREEVFPFWQNKSVDEFCEGQYREADLWEMSGES
FVSDCSYHAVNGGGDSNPGYDVILMKKGMLDIQREAREKLEQLDYANPED
IDKIYFYKSVIETAEGVMIYARRLSAYAAELAARETDPRRKAELQKISEV
NARVPAHAPSNFWEAIQAVWTVESLLVVEENQTGMSIGRVDQYMYPFYRA
DIDSGRLTEYEAFDLAGCMLVKMSEMMWITSEGASKFFAGYQPFVNMCVG
GVTREGHDATNDLTYMLMDAVRHVRIYQPTLATRVHNKSPQKYLKKIVDV
IRSGMGFPAVHFDDAHIKMMLAKGVSIEDARDYCLMGCVEPQKSGRLYQW
TSTGYTQWPICIELVLNHGVPLWYGKKVTPDMGDLSQYDTYEKFEAAVKE
QIRWITKNTSVATVISQRAHRELAPKPLMSLMYEGCMESGRDVSAGGAMY
NFGPGVVWSGLATYVDSMAAIKKLVYDDRKYTLAQLNEALKADFAGYDQI
LADCLAAPKYGNDDDYADMIAADLVHFTETEHRKYKTLYSVLSHGTLSIS
NNTPFGQLLGASANGRRAWMPLSDGISPTQGADYKGPTAIIKSVSKMAND
NMNIGMVHNFKLMSGLLDTPEGENGLITLIRTACMLGNGEMQFNYLDNEL
LLDAQKHPEKYRDLVVRVAGYSAFFVELCKDVQDEIISRTMLHGF
Ligand information
Ligand IDBTL
InChIInChI=1S/C5H12NO/c1-6(2,3)4-5-7/h5H,4H2,1-3H3/q+1
InChIKeySXKNCCSPZDCRFD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=CC[N+](C)(C)C
CACTVS 3.341
OpenEye OEToolkits 1.5.0		C[N+](C)(C)CC=O
FormulaC5 H12 N O
NameBETAINE ALDEHYDE;
[FORMYLMETHYL]TRIMETHYL-AMMONIUM;
N,N,N-TRIMETHYL AMMONIUM ACETALDEHYDE
ChEMBLCHEMBL1231491
DrugBankDB04401
ZINCZINC000100015771
PDB chain6nd3 Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6nd3 Structure-Guided Identification of a Small Molecule That Inhibits Anaerobic Choline Metabolism by Human Gut Bacteria.
Resolution2.364 Å
Binding residue
(original residue number in PDB)		Y208 F395 C489 E491 T502
Binding residue
(residue number reindexed from 1)		Y157 F344 C438 E440 T451
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.59,IC50=26uM
Enzymatic activity
Catalytic site (original residue number in PDB) F395 G488 C489 G821
Catalytic site (residue number reindexed from 1) F344 G437 C438 G770
Enzyme Commision number 4.3.99.4: choline trimethylamine-lyase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0016829 lyase activity
GO:0016840 carbon-nitrogen lyase activity
GO:0033265 choline binding
GO:0042803 protein homodimerization activity
Biological Process
GO:0042426 choline catabolic process
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6nd3, PDBe:6nd3, PDBj:6nd3
PDBsum6nd3
PubMed30557011
UniProtQ30W70|CUTC_OLEA2 Choline trimethylamine-lyase (Gene Name=cutC)

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