Structure of PDB 7kgm Chain A Binding Site BS01

Receptor Information
>7kgm Chain A (length=512) Species: 637910 (Citrobacter rodentium ICC168) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LEQSPVTGIMAGIKPLPEGIDIGSVRQQLLTGLPSGYTPAYMDQLTLLYA
AREMKPMWENRDAVRAFQQQLAEVAIAGFQPQFTRWVELLTDPAVSGQAR
DVVLSDAMMGYLQFVAGIPVNGNRWLYSNKPYKLATPALSVINQWQLALD
NGELPRFIASLAPAHPQYARMHQSLLALVGDSRPWPQLRSAATLRPGQWS
SDVPALREILKRSGMLPAAYDRELVAAVKQFQAWQGLGADGAIGPATRYW
MNVTPAQRAGGLALNIQRLRLLPAELSTGIMVNIPAYSLVYYQNGSQVLA
SRVIVGRPDRKTPMMSSALNNVVVNPPWNVPPTLARKDILPKLWNDPGYL
ERHGYTVMRSKDAIDPWQVDWSTITPSNLPFRFQQAPGAHNSLGRYKFNM
PSDAIYLHDTPNHTLFSKDARALSSGCVRVNKASELANMLLQDAGWNDTR
ISDALKQGNTRYVTIRQTIPVNLYYLTAFVGADGRTQYRTDIYNYDLTAR
SSAQIVEKAEQL
Ligand information
Ligand ID1RG
InChIInChI=1S/C22H27N3O7S/c1-10-17(15(9-26)11(2)27)25-18(22(31)32)19(10)33-14-7-16(23-8-14)20(28)24-13-5-3-4-12(6-13)21(29)30/h3-6,9-11,14-17,23,25,27H,7-8H2,1-2H3,(H,24,28)(H,29,30)(H,31,32)/t10-,11-,14+,15-,16+,17-/m1/s1
InChIKeyPGRRQYXTRXQDDJ-SKHPLXCOSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)c1cc(ccc1)NC(=O)C3NCC(SC2=C(C(=O)O)NC(C2C)C(C=O)C(O)C)C3
OpenEye OEToolkits 1.7.6C[C@@H]1[C@@H](NC(=C1S[C@H]2C[C@H](NC2)C(=O)Nc3cccc(c3)C(=O)O)C(=O)O)[C@H](C=O)[C@@H](C)O
OpenEye OEToolkits 1.7.6CC1C(NC(=C1SC2CC(NC2)C(=O)Nc3cccc(c3)C(=O)O)C(=O)O)C(C=O)C(C)O
CACTVS 3.370C[CH](O)[CH](C=O)[CH]1NC(=C(S[CH]2CN[CH](C2)C(=O)Nc3cccc(c3)C(O)=O)[CH]1C)C(O)=O
CACTVS 3.370C[C@@H](O)[C@@H](C=O)[C@@H]1NC(=C(S[C@@H]2CN[C@@H](C2)C(=O)Nc3cccc(c3)C(O)=O)[C@@H]1C)C(O)=O
FormulaC22 H27 N3 O7 S
Name(4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid;
ERTAPENEM, bound form PRE-ISOMERIZED
ChEMBL
DrugBank
ZINCZINC000103522323
PDB chain7kgm Chain A Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7kgm Structural and Cellular Insights into the l,d-Transpeptidase YcbB as a Therapeutic Target in Citrobacter rodentium, Salmonella Typhimurium, and Salmonella Typhi Infections.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		P437 Y516 S535 C537
Binding residue
(residue number reindexed from 1)		P331 Y406 S425 C427
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004180 carboxypeptidase activity
GO:0016740 transferase activity
Biological Process
GO:0000270 peptidoglycan metabolic process
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0071555 cell wall organization

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:7kgm, PDBe:7kgm, PDBj:7kgm
PDBsum7kgm
PubMed33139287
UniProtD2TS62

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