Structure of PDB 7f3v Chain B Binding Site BS01

Receptor Information
>7f3v Chain B (length=241) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLIVPQWPQPKGVAACSSTRIGGVSLPPYDSLNLGAHCGDNPDHVEENRK
RLFAAGNLPSKPVWLEQVHGKDVLKLTGEPYASKRADASYSNTPGTVCAV
MTADALPVLFCNRAGTEVAAAHAGWRGLCAGVLEETVSCFADNPENILAW
LGPAIGPRAFEVGGEVREAFMAVDAKASAAFIQHGDKYLADIYQLARQRL
ANVGVEQIFGGDRCTYTENETFFSYRRDKTTGRMASFIWLI
Ligand information
Ligand IDEPZ
InChIInChI=1S/C20H31N3O19P2/c1-7(18(30)31)38-16-12(21-8(2)25)19(40-9(5-24)14(16)28)41-44(35,36)42-43(33,34)37-6-10-13(27)15(29)17(39-10)23-4-3-11(26)22-20(23)32/h3-4,7,9-10,12-17,19,24,27-29H,5-6H2,1-2H3,(H,21,25)(H,30,31)(H,33,34)(H,35,36)(H,22,26,32)/t7-,9-,10-,12-,13-,14-,15-,16-,17-,19-/m1/s1
InChIKeyNQBRVZNDBBMBLJ-MQTLHLSBSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C1C=CN(C(=O)N1)C2OC(C(O)C2O)COP(=O)(OP(=O)(OC3OC(C(O)C(OC(C(=O)O)C)C3NC(=O)C)CO)O)O
CACTVS 3.370C[CH](O[CH]1[CH](O)[CH](CO)O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH]1NC(C)=O)C(O)=O
CACTVS 3.370C[C@@H](O[C@H]1[C@H](O)[C@@H](CO)O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@@H]1NC(C)=O)C(O)=O
OpenEye OEToolkits 1.7.2CC(C(=O)O)OC1C(C(OC(C1O)CO)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C
OpenEye OEToolkits 1.7.2C[C@H](C(=O)O)O[C@@H]1[C@H]([C@H](O[C@@H]([C@H]1O)CO)O[P@](=O)(O)O[P@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C
FormulaC20 H31 N3 O19 P2
Name(2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoic acid
ChEMBL
DrugBank
ZINCZINC000008551287
PDB chain7f3v Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7f3v Structural Basis for the Peptidoglycan-Editing Activity of YfiH.
Resolution1.47 Å
Binding residue
(original residue number in PDB)		H71 T104 A105 A107 H124 G126 W127 R128 E163 V164 G165 K189 Y227 R228
Binding residue
(residue number reindexed from 1)		H69 T102 A103 A105 H122 G124 W125 R126 E161 V162 G163 K187 Y225 R226
Annotation score1
Enzymatic activity
Enzyme Commision number 1.10.3.-
2.4.2.1: purine-nucleoside phosphorylase.
2.4.2.28: S-methyl-5'-thioadenosine phosphorylase.
3.5.4.4: adenosine deaminase.
Gene Ontology
Molecular Function
GO:0004000 adenosine deaminase activity
GO:0004731 purine-nucleoside phosphorylase activity
GO:0005507 copper ion binding
GO:0016491 oxidoreductase activity
GO:0016682 oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor
GO:0016740 transferase activity
GO:0016787 hydrolase activity
GO:0017061 S-methyl-5-thioadenosine phosphorylase activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0046936 2'-deoxyadenosine deaminase activity
Biological Process
GO:0000270 peptidoglycan metabolic process
Cellular Component
GO:0005829 cytosol
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:7f3v, PDBe:7f3v, PDBj:7f3v
PDBsum7f3v
PubMed35164571
UniProtP33644|PURNU_ECOLI Purine nucleoside phosphorylase YfiH (Gene Name=yfiH)

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