Structure of PDB 4dki Chain B Binding Site BS01

Receptor Information
>4dki Chain B (length=632) Species: 93062 (Staphylococcus aureus subsp. aureus COL) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKDKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLG
VKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWK
LDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIV
PKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYL
SDFAKKFHLTTNETESRNYPLEKATSHLLGYVGPINSEELKQKEYKGYKD
DAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDI
QLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYG
MSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTS
YKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALEL
GSKKFEKGMKKLGVGEDIPSDYPFYNAQISKNLDNEILLADSGYGQGEIL
INPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGM
QQVVNKTHKEDIYRSYANLIGKSGTAELKRQIGWFISYDKDNPNMMMAIN
VKDVMASYNAKISGKVYDELYENGNKKYDIDE
Ligand information
Ligand IDRB6
InChIInChI=1S/C20H24N8O6S2/c21-20-25-15(27-36-20)14(26-34)16(30)23-12(7-29)17-24-13(19(32)33)10(8-35-17)5-9-2-4-28(18(9)31)11-1-3-22-6-11/h2,7,11-12,17,22,24,34H,1,3-6,8H2,(H,23,30)(H,32,33)(H2,21,25,27)/b26-14-/t11-,12-,17-/m1/s1
InChIKeyMYAXGJQBOYOEHQ-SWBIIUODSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1snc(n1)C(=NO)C(=O)N[CH](C=O)[CH]2NC(=C(CS2)CC3=CCN([CH]4CCNC4)C3=O)C(O)=O
OpenEye OEToolkits 1.7.6C1CNC[C@@H]1N2CC=C(C2=O)CC3=C(N[C@H](SC3)[C@@H](C=O)NC(=O)/C(=N\O)/c4nc(sn4)N)C(=O)O
OpenEye OEToolkits 1.7.6C1CNCC1N2CC=C(C2=O)CC3=C(NC(SC3)C(C=O)NC(=O)C(=NO)c4nc(sn4)N)C(=O)O
ACDLabs 12.01O=C(O)C=1NC(SCC=1CC2=CCN(C2=O)C3CCNC3)C(C=O)NC(=O)C(=N\O)/c4nc(sn4)N
CACTVS 3.370Nc1snc(n1)C(=N/O)/C(=O)N[C@H](C=O)[C@@H]2NC(=C(CS2)CC3=CCN([C@@H]4CCNC4)C3=O)C(O)=O
FormulaC20 H24 N8 O6 S2
Name(2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-pyr rolidin-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid;
BAL 9141, bound form;
ceftobiprole, bound form
ChEMBL
DrugBank
ZINCZINC000103555189
PDB chain4dki Chain B Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4dki Structural Insights into the Anti-methicillin-resistant Staphylococcus aureus (MRSA) Activity of Ceftobiprole.
Resolution2.9 Å
Binding residue
(original residue number in PDB)
S403 K406 Y446 S462 N464 Y519 Q521 S598 G599 T600 E602
Binding residue
(residue number reindexed from 1)
S379 K382 Y422 S438 N440 Y494 Q496 S573 G574 T575 E577
Annotation score1
Enzymatic activity
Enzyme Commision number 3.4.16.4: serine-type D-Ala-D-Ala carboxypeptidase.
Gene Ontology
Molecular Function
GO:0004180 carboxypeptidase activity
GO:0008658 penicillin binding
GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity
GO:0071972 peptidoglycan L,D-transpeptidase activity
Biological Process
GO:0046677 response to antibiotic
GO:0071555 cell wall organization
Cellular Component
GO:0016020 membrane

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:4dki, PDBe:4dki, PDBj:4dki
PDBsum4dki
PubMed22815485
UniProtA0A0H2WXF8

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