Structure of PDB 4b52 Chain A Binding Site BS05

Receptor Information
>4b52 Chain A (length=304) Species: 1406 (Paenibacillus polymyxa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATGTGKGVLGDTKSFTTTASGSSYQLKDTTRGNGVVTYTASNRQSIPGTI
LTDADNVWNDPAGVDAHTYAAKTYDYYKAKFGRNSIDGRGLQLRSTVHYG
SRYNNAFWNGSQMTYGDGDGSTFIAFSGDPDVVGHELTHGVTEYTSNLEY
YGESGALNEAFSDVIGNDIQRKNWLVGDDIYTPNIAGDALRSMSNPTLYD
QPDHYSNLYTGSSDNGGVHTNSGIINKAYYLLAQGGTFHGVTVNGIGRDA
AVQIYYSAFTNYLTSSSDFSNARAAVIQAAKDQYGANSAEATAAAKSFDA
VGVN
Ligand information
Ligand IDRDF
InChIInChI=1S/C23H34N3O10P/c1-11(2)8-16(26-37(33,34)36-23-20(29)19(28)18(27)12(3)35-23)21(30)25-17(22(31)32)9-13-10-24-15-7-5-4-6-14(13)15/h4-7,10-12,16-20,23-24,27-29H,8-9H2,1-3H3,(H,25,30)(H,31,32)(H2,26,33,34)/t12-,16-,17-,18-,19+,20+,23-/m0/s1
InChIKeyZPHBZEQOLSRPAK-XLCYBJAPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1C(C(C(C(O1)OP(=O)(NC(CC(C)C)C(=O)NC(Cc2c[nH]c3c2cccc3)C(=O)O)O)O)O)O
ACDLabs 10.04O=P(OC1OC(C(O)C(O)C1O)C)(O)NC(C(=O)NC(C(=O)O)Cc3c2ccccc2nc3)CC(C)C
OpenEye OEToolkits 1.5.0C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[P@](=O)(N[C@@H](CC(C)C)C(=O)N[C@@H](Cc2c[nH]c3c2cccc3)C(=O)O)O)O)O)O
CACTVS 3.341CC(C)C[C@H](N[P@@](O)(=O)O[C@@H]1O[C@@H](C)[C@H](O)[C@@H](O)[C@H]1O)C(=O)N[C@@H](Cc2c[nH]c3ccccc23)C(O)=O
CACTVS 3.341CC(C)C[CH](N[P](O)(=O)O[CH]1O[CH](C)[CH](O)[CH](O)[CH]1O)C(=O)N[CH](Cc2c[nH]c3ccccc23)C(O)=O
FormulaC23 H34 N3 O10 P
NameN-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN;
PHOSPHORAMIDON
ChEMBLCHEMBL479579
DrugBankDB02557
ZINCZINC000004475339
PDB chain4b52 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4b52 Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa
Resolution1.76 Å
Binding residue
(original residue number in PDB)		N104 N105 A106 F123 F126 H135 E136 H139 E159 L190 R191 H219
Binding residue
(residue number reindexed from 1)		N104 N105 A106 F123 F126 H135 E136 H139 E159 L190 R191 H219
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H135 E136 H139 Y150 E159 D214 H219
Catalytic site (residue number reindexed from 1) H135 E136 H139 Y150 E159 D214 H219
Enzyme Commision number 3.4.24.-
Gene Ontology
Molecular Function
GO:0004222 metalloendopeptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:4b52, PDBe:4b52, PDBj:4b52
PDBsum4b52
PubMed23275160
UniProtE3E6L0

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