Structure of PDB 6pd2 Chain D Binding Site BS04

Receptor Information
>6pd2 Chain D (length=608) Species: 243275 (Treponema denticola ATCC 35405) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIKQAVILAGGLTKTMPKGFLEIGGTAIVEQSVQKLLAHGIEKIVIGTGH
CNEYYDNLAKKYPAIITVKNENYANTGSMGTLEVCASFVNESFLLLESDL
IYDSAGLFSLINDERKNLILASGATKSGDEVYLEADEKNCLTGLSKNRDA
LKNIFGELVGITKLTKSTLDKMCAYAKIHHSDLPKMEYEHALLEAAKTIP
VAIKRIEYFVWREIDNEDHLEMAVKNIYPHIVENEKLRAVRREVLLNPGP
ATTTDSVKYAQVSADICPREKAFGDLMQWLCDELKLFALASETNPDEYET
VMFGCSGTGADEVMVSSCVPDTGRLLVIDNGSYGARMAKIADIYKIPMDI
FKSSTYEPLDLQKLEAEFATKKYTHLACVYHETTTGLLNPLHIICPMAKK
YGMVTIVDAVSAYCGMPMDLKSLGIDFMASTSNKNIQGMAGVGFVICNKA
ELEKTKDYPMRNYYLNLYDQYAYFAKTHQTRFTPPVQTMYALRQAVLETK
QETVQKRYERYTACWNILVAAIKKLGLKMLVKEEHQSHFITAILEPETPK
YSFEALHDFAAEHSFTIYPGKLGNIDTFRIANIGDIQPEEMRRFTVKLKE
YMNGIGVG
Ligand information
Ligand ID0RC
InChIInChI=1S/C11H20N4O10P2/c12-2-4-26(19,20)25-27(21,22)23-5-6-8(16)9(17)10(24-6)15-3-1-7(13)14-11(15)18/h1,3,6,8-10,16-17H,2,4-5,12H2,(H,19,20)(H,21,22)(H2,13,14,18)/t6-,8-,9-,10-/m1/s1
InChIKeyFBADRUOBFLBKJQ-PEBGCTIMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@@](=O)(CCN)O)O)O
CACTVS 3.341NCC[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=NC2=O)N
CACTVS 3.341NCC[P@](O)(=O)O[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=NC2=O)N
ACDLabs 10.04O=P(O)(OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O)CCN
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(CCN)O)O)O
FormulaC11 H20 N4 O10 P2
Name5'-O-[(S)-{[(R)-(2-aminoethyl)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine
ChEMBL
DrugBank
ZINCZINC000008220008
PDB chain6pd2 Chain D Residue 705 [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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PDB6pd2 The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		L8 A9 G10 G11 T83 G84 S85 T88 E104 S105 D106 D136 E196 E220 D222
Binding residue
(residue number reindexed from 1)		L8 A9 G10 G11 T76 G77 S78 T81 E97 S98 D99 D129 E189 E213 D215
Annotation score1
Enzymatic activity
Enzyme Commision number 2.6.1.37: 2-aminoethylphosphonate--pyruvate transaminase.
2.7.7.107: (2-aminoethyl)phosphonate cytidylyltransferase.
Gene Ontology
Molecular Function
GO:0008483 transaminase activity
GO:0016779 nucleotidyltransferase activity
GO:0046872 metal ion binding
GO:0047304 2-aminoethylphosphonate-pyruvate transaminase activity
Biological Process
GO:0019700 organic phosphonate catabolic process
GO:0032923 organic phosphonate biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6pd2, PDBe:6pd2, PDBj:6pd2
PDBsum6pd2
PubMed31420548
UniProtQ73MU2|PNTCW_TREDE Bifunctional 2-aminoethylphosphonate cytidylyltransferase/aminotransferase (Gene Name=pntC)

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