Structure of PDB 7kdy Chain A Binding Site BS04

Receptor Information
>7kdy Chain A (length=661) Species: 2689386 (Streptomyces tokunonensis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RGRKVYFVGLNEYPFLPLVAGLLRTYAEQDERIAAAYDFQEPVFLVAPVQ
EMADGIVEPDVLALSCYVWNFRRQMKVAKLVKERYPNVLVVAGGPHVPDR
PGNFFEKHPYVDVLAHGEGEVAFRELLATRLSDHPDYTAVPGVSVRRGTE
AVVGPKAKRLPRLIDTPSPYLLGVMDGAVATCRERGLRFYALWETNRGCP
YSCSFCDWGSATMSTLRKFEDERLQDEIEWFARHDVEDLFICDANFGIMP
RDLEIAHALAEARGELGAPRQVRVNFAKNSNDRVFDISKTWHDADLLMGT
TLSMQSTDMDVLEAIDRKNIGLDNYRKLQQRYAAENIHTYTELILGLPME
TARSFRDGIGSLLEAGNHEDLRVYELGILPNAPLNTPEKIEQYGLRTVPK
RMYVERPGTPDDEAETFEMVMETNAMPRDAWVESFSFIQAVQFLHNGCYT
RYLSIFLRQEHGIGYTRFYEGLQDYFTGRPDTVLGALYLRMRSLYHDYID
MPALPLANLVASQPDMAADLAPYGRRRGWTIDNWGWLRIATDFDRFHTEL
REYLATLGLDARLEDVLRFQQDVMLRPDYSPELGKSAEYAHDWPGYFAGG
LLRPRRVRVAYGDQSFGANGRYRPVPGDLKAFTMAAIGTSYPVSRMGHFC
HRFESAEVTSL
Ligand information
Ligand IDWCD
InChIInChI=1S/C18H29N3O7S/c1-18(2,9-22)15(25)16(26)20-4-3-12(23)19-5-6-29-11-7-10-8-13(24)21(10)14(11)17(27)28/h10-11,14-15,22,25H,3-9H2,1-2H3,(H,19,23)(H,20,26)(H,27,28)/t10-,11+,14-,15-/m0/s1
InChIKeyXJMYKDFZQNYDFC-JLUCKKNBSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)(CO)[C@@H](O)C(=O)NCCC(=O)NCCS[C@@H]1C[C@H]2CC(=O)N2[C@@H]1C(O)=O
ACDLabs 12.01C(O)C(C)(C)C(O)C(NCCC(NCCSC1C(N2C(CC2C1)=O)C(O)=O)=O)=O
OpenEye OEToolkits 2.0.7CC(C)(CO)[C@H](C(=O)NCCC(=O)NCCS[C@@H]1C[C@H]2CC(=O)N2[C@@H]1C(=O)O)O
OpenEye OEToolkits 2.0.7CC(C)(CO)C(C(=O)NCCC(=O)NCCSC1CC2CC(=O)N2C1C(=O)O)O
CACTVS 3.385CC(C)(CO)[CH](O)C(=O)NCCC(=O)NCCS[CH]1C[CH]2CC(=O)N2[CH]1C(O)=O
FormulaC18 H29 N3 O7 S
Name(2R,3R,5R)-3-{[2-({N-[(2R)-2,4-dihydroxy-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-7-oxo-1-azabicyclo[3.2.0]heptane-2-carboxylic acid;
(2R)-pantetheinylated carbapenam
ChEMBL
DrugBank
ZINC
PDB chain7kdy Chain A Residue 705 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7kdy Structure of a B 12 -dependent radical SAM enzyme in carbapenem biosynthesis.
Resolution1.939 Å
Binding residue
(original residue number in PDB)
R280 Y381 N515 Y652
Binding residue
(residue number reindexed from 1)
R273 Y374 N508 Y641
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0008168 methyltransferase activity
GO:0031419 cobalamin binding
GO:0046872 metal ion binding
GO:0051536 iron-sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0032259 methylation
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:7kdy, PDBe:7kdy, PDBj:7kdy
PDBsum7kdy
PubMed35110734
UniProtA0A6B9HEI0

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