Structure of PDB 3rc9 Chain A Binding Site BS03

Receptor Information
>3rc9 Chain A (length=314) Species: 46161 (Actinomadura kijaniata) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NPIRVGVIGCADIAWRRALPALEAEPLTEVTAIASRRWDRAKRFTERFGG
EPVEGYPALLERDDVDAVYVPLPAVLHAEWIDRALRAGKHVLAEAPLTTD
RPQAERLFAVARERGLLLMENFMFLHHPQHRQVADMLDEGVIGEIRSFAA
SFTIPPVGGGALLDIGVYPIRAAGLFLGADLEFVGAVLRHERDRDVVVGG
NALLTTRQGVTAQLTFGMEHAYTNNYEFRGSTGRLWMNRVFTPPATYQPV
VHIERQDHAEQFVLPAHDQFAKSIRAFAQAVLSGEHPREWSEDSLRQASL
VDAVRTGARDIYFP
Ligand information
Ligand IDTLO
InChIInChI=1S/C16H20N2O11P2/c1-10-8-18(16(21)17-15(10)20)14-7-12(19)13(27-14)9-26-30(22,23)29-31(24,25)28-11-5-3-2-4-6-11/h2-6,8,12-14,19H,7,9H2,1H3,(H,22,23)(H,24,25)(H,17,20,21)/t12-,13+,14+/m0/s1
InChIKeyBANJVYKYIQPYKP-BFHYXJOUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)Oc3ccccc3)O2)C(=O)NC1=O
OpenEye OEToolkits 1.7.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@@](=O)(O)Oc3ccccc3)O
OpenEye OEToolkits 1.7.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)Oc3ccccc3)O
CACTVS 3.370CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)Oc3ccccc3)O2)C(=O)NC1=O
ACDLabs 12.01O=P(Oc1ccccc1)(O)OP(=O)(O)OCC3OC(N2C(=O)NC(=O)C(=C2)C)CC3O
FormulaC16 H20 N2 O11 P2
Name5'-O-[(S)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]thymidine;
thymidine diphosphate phenol
ChEMBL
DrugBank
ZINCZINC000058633056
PDB chain3rc9 Chain A Residue 337 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3rc9 Combined Structural and Functional Investigation of a C-3''-Ketoreductase Involved in the Biosynthesis of dTDP-l-Digitoxose.
Resolution1.91 Å
Binding residue
(original residue number in PDB)		I20 R23 R24 F159 I161 P162 Y186 Y240 T260
Binding residue
(residue number reindexed from 1)		I13 R16 R17 F152 I154 P155 Y168 Y222 T242
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) A102 Y186
Catalytic site (residue number reindexed from 1) A95 Y168
Enzyme Commision number 1.1.1.384: dTDP-3,4-didehydro-2,6-dideoxy-alpha-D-glucose 3-reductase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016491 oxidoreductase activity
Biological Process
GO:0017000 antibiotic biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3rc9, PDBe:3rc9, PDBj:3rc9
PDBsum3rc9
PubMed21598943
UniProtB3TMR8|KIJDR_ACTKI dTDP-3,4-didehydro-2,6-dideoxy-alpha-D-glucose 3-reductase (Gene Name=KijD10)

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