Structure of PDB 4zm4 Chain E Binding Site BS01

Receptor Information
>4zm4 Chain E (length=425) Species: 68249 (Streptomyces pactum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TNAESLDGIKSVIAGGVSSSMRAAAVPLPLVVRSAGGCLLRDVEDGEIID
LNMGYGPHLFGYADREVLDAVADQFAKGHMTGLPHELDARAGALIAELVP
GVEQVRFANSGTEAVASALRLARATTGRTLVVTFEGHYHGWSETVLRATR
PTDVVPGALGMIPEALAHTVQLGWNDPDALRELFARDGDRIAAVIVEPVL
ANAGVIPPAPGFLQLLRELTGRSGAMLVFDEVITGFRVARGGAQERYGVE
PDLTVLSRVMGGGFPVAAFGGRRHAMRMLASNEAHHAGVYAGNHAALRAV
VAMLGKIRSLPDLYERLEDTGQYMEDTVREVFATEKRPVHINRVGTLMSV
ALLKGSAEPSAEPRDLRQLAALVDFPRHRRLQTLAQKEGVYFHPNALEPW
FLSTAHTRDVIDKVAGALQRSLVGL
Ligand information
Ligand IDP3B
InChIInChI=1S/C15H19N2O9P/c1-7-13(19)10(9(4-16-7)6-26-27(23,24)25)5-17-11-2-8(15(21)22)3-12(18)14(11)20/h2,4-5,12,14,16,18-20H,3,6H2,1H3,(H,21,22)(H2,23,24,25)/b10-5-,17-11+/t12-,14-/m1/s1
InChIKeyKOPNIGHVUGDBMS-FEZKIMOASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CC1=C(C(=CN=C2C=C(CC(C2O)O)C(=O)O)C(=CN1)COP(=O)(O)O)O
CACTVS 3.385CC1=C(O)C(=CN=C2C=C(C[CH](O)[CH]2O)C(O)=O)C(=CN1)CO[P](O)(O)=O
OpenEye OEToolkits 1.9.2CC1=C(/C(=C\N=C\2/C=C(C[C@H]([C@@H]2O)O)C(=O)O)/C(=CN1)COP(=O)(O)O)O
ACDLabs 12.01OP(O)(=O)OCC1=CNC(C)=C(C1=[C@H]\N=C2/C=C(C(O)=O)CC(C2O)O)O
CACTVS 3.385CC1=C(O)C(=C/N=C2C=C(C[C@@H](O)[C@@H]2O)C(O)=O)\C(=CN1)CO[P](O)(O)=O
FormulaC15 H19 N2 O9 P
Name(3E,4R,5R)-4,5-dihydroxy-3-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}cyclohex-1-ene-1-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000263620661
PDB chain4zm4 Chain E Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4zm4 Mechanism-Based Trapping of the Quinonoid Intermediate by Using the K276R Mutant of PLP-Dependent 3-Aminobenzoate Synthase PctV in the Biosynthesis of Pactamycin.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		S28 R31 G120 T121 Y147 G149 N220 D248 V250 R276
Binding residue
(residue number reindexed from 1)		S19 R22 G111 T112 Y138 G140 N202 D230 V232 R258
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) V26 Y147 E215 D248 I251 R276 P417
Catalytic site (residue number reindexed from 1) V17 Y138 E197 D230 I233 R258 P399
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0008483 transaminase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0009058 biosynthetic process

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:4zm4, PDBe:4zm4, PDBj:4zm4
PDBsum4zm4
PubMed26426567
UniProtA8R0K5

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