Structure of PDB 1dak Chain A Binding Site BS02

Receptor Information
>1dak Chain A (length=224) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYKPVASGSEKTPEGL
RNSDALALQRNSSLQLDYATVNPYTFAEPTSPHIISAQEGRPIESLVMSA
GLRALEQQADWVLVEGAGGWFTPLSDTFTFADWVTQEQLPVILVVGVKLG
CINHAMLTAQVIQHAGLTLAGWVANDVTPPGKRHAEYMTTLTRMIPAPLL
GEIPWLAENPENAATGKYINLALL
Ligand information
Ligand IDDPU
InChIInChI=1S/C10H21N2O7P/c1-7(11)8(5-3-2-4-6-9(13)14)12-10(15)19-20(16,17)18/h7-8H,2-6,11H2,1H3,(H,12,15)(H,13,14)(H2,16,17,18)/t7-,8+/m0/s1
InChIKeyUJJZZEABROBUCE-JGVFFNPUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C(CCCCCC(=O)O)NC(=O)OP(=O)(O)O)N
CACTVS 3.341C[CH](N)[CH](CCCCCC(O)=O)NC(=O)O[P](O)(O)=O
ACDLabs 10.04O=C(OP(=O)(O)O)NC(CCCCCC(=O)O)C(N)C
OpenEye OEToolkits 1.5.0C[C@@H]([C@@H](CCCCCC(=O)O)NC(=O)OP(=O)(O)O)N
CACTVS 3.341C[C@H](N)[C@@H](CCCCCC(O)=O)NC(=O)O[P](O)(O)=O
FormulaC10 H21 N2 O7 P
NameMIXED CARBAMIC PHOSPHORIC ACID ANHYDRIDE OF 7,8-DIAMINONONANIC ACID
ChEMBL
DrugBankDB02927
ZINCZINC000002046974
PDB chain1dak Chain A Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1dak Snapshot of a phosphorylated substrate intermediate by kinetic crystallography.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		T11 K15 K37 S41 P79 A117 G118
Binding residue
(residue number reindexed from 1)		T11 K15 K37 S41 P79 A117 G118
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) T11 E12 K15 T16 K37 S41 D54 E115
Catalytic site (residue number reindexed from 1) T11 E12 K15 T16 K37 S41 D54 E115
Enzyme Commision number 6.3.3.3: dethiobiotin synthase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004141 dethiobiotin synthase activity
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
Biological Process
GO:0009102 biotin biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1dak, PDBe:1dak, PDBj:1dak
PDBsum1dak
PubMed9576910
UniProtP13000|BIOD1_ECOLI ATP-dependent dethiobiotin synthetase BioD 1 (Gene Name=bioD1)

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