Structure of PDB 5k1d Chain A Binding Site BS01

Receptor Information
>5k1d Chain A (length=359) Species: 548 (Klebsiella aerogenes) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HHGEASPVDPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVAN
RESGAGVSEQTLFEIGSVSKTLTATLGAYAVVKGAMQLDDKASRHAPWLK
GSAFDSITMGELATYSAGGLPLQFPEEVDSSEKMRAYYRQWAPVYSPGSH
RQYSNPSIGLFGHLAASSLKQPFAPLMEQTLLPGLGMHHTYVNVPKQAMA
SYAYGYSKEDKPIRVNPGMLADEAYGIKTSSADLLRFVKANIGGVDDKAL
QQAISLTHQGHYSVGGMTQGLGWESYAYPVTEQTLLAGNSAKVILEANPT
AAPRESQVLFNKTGSTNGFGAYVAFVPARGIGIVMLANRNYPIEARIKAA
HAILAQLAG
Ligand information
Ligand ID5GP
InChIInChI=1S/C10H14N5O8P/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(23-9)1-22-24(19,20)21/h2-3,5-6,9,16-17H,1H2,(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyRQFCJASXJCIDSX-UUOKFMHZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3O)COP(=O)(O)O
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H14 N5 O8 P
NameGUANOSINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL283807
DrugBankDB01972
ZINCZINC000002159505
PDB chain5k1d Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5k1d GMP and IMP Are Competitive Inhibitors of CMY-10, an Extended-Spectrum Class C beta-Lactamase.
Resolution1.94 Å
Binding residue
(original residue number in PDB)		S65 L120 Q121 Y151 I292 L293 T313 G314 S315 I343
Binding residue
(residue number reindexed from 1)		S67 L122 Q123 Y153 I294 L295 T313 G314 S315 I343
Annotation score1
Binding affinityMOAD: Ki=20.8uM
PDBbind-CN: -logKd/Ki=4.68,Ki=20.8uM
Enzymatic activity
Catalytic site (original residue number in PDB) S65 K68 M107 E109 F122 Y151 G157 E272 K312 S315
Catalytic site (residue number reindexed from 1) S67 K70 M109 E111 F124 Y153 G159 E274 K312 S315
Enzyme Commision number 3.5.2.6: beta-lactamase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0008800 beta-lactamase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
Biological Process
GO:0017001 antibiotic catabolic process
GO:0046677 response to antibiotic
Cellular Component
GO:0030288 outer membrane-bounded periplasmic space

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5k1d, PDBe:5k1d, PDBj:5k1d
PDBsum5k1d
PubMed28242658
UniProtQ99QC1

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