Structure of PDB 3vpd Chain B Binding Site BS01

Receptor Information
>3vpd Chain B (length=268) Species: 274 (Thermus thermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLAILYDRIRPDERMLFERAEALGLPYKKVYVPALPMVLGERPEALEGVT
VALERCVSQSRGLAAARYLTALGIPVVNRPEVIEACGDKWATSVALAKAG
LPQPKTALATDREEALRLMEAFGYPVVLKPVIGSWGRLLAKVTDRAAAEA
LLEHKEVLGGFQHQLFYIQEYVEKPGRDIRVFVVGERAIAAIYRQAENCP
LTEEIARLSVGAAEAVGGGVVAVDLFESERGLLVNEVNHTMEFKNSVHTT
GVDIPGEILRYAWEVARG
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain3vpd Chain B Residue 301 [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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PDB3vpd Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		K129 Q169 E170 Y171 V172 K174 D178 R180 R194 F239 E249
Binding residue
(residue number reindexed from 1)		K129 Q169 E170 Y171 V172 K174 D178 R180 R194 F226 E236
Annotation score3
Enzymatic activity
Enzyme Commision number 6.3.2.43: [amino-group carrier protein]--L-2-aminoadipate ligase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0018169 ribosomal S6-glutamic acid ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0009085 lysine biosynthetic process
GO:0009432 SOS response
GO:0018410 C-terminal protein amino acid modification
GO:0019878 lysine biosynthetic process via aminoadipic acid
GO:0036211 protein modification process
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3vpd, PDBe:3vpd, PDBj:3vpd
PDBsum3vpd
PubMed23434852
UniProtQ5SH23|LYSX_THET8 Alpha-aminoadipate--LysW ligase LysX (Gene Name=lysX)

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