Structure of PDB 3rc7 Chain A Binding Site BS01

Receptor Information
>3rc7 Chain A (length=325) Species: 46161 (Actinomadura kijaniata) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NPIRVGVIGCADIAWRRALPALEAEPLTEVTAIASRRWDRAKRFTERFGG
EPVEGYPALLERDDVDAVYVPLPAVLHAEWIDRALRAGKHVLAEKPLTTD
RPQAERLFAVARERGLLLMENFMFLHHPQHRQVADMLDEGVIGEIRSFAA
SFTIPPKPQGDIRYQADVGGGALLDIGVFPIRAAGLFLGADLEFVGAVLR
HERDRDVVVGGNALLTTRQGVTAQLTFGMEHAYTNNYEFRGSTGRLWMNR
VFTPPATYQPVVHIERQDHAEQFVLPAHDQFAKSIRAFAQAVLSGEHPRE
WSEDSLRQASLVDAVRTGARDIYFP
Ligand information
Ligand IDNAP
InChIInChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyXJLXINKUBYWONI-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
FormulaC21 H28 N7 O17 P3
NameNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE;
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
ChEMBLCHEMBL295069
DrugBankDB03461
ZINC
PDB chain3rc7 Chain A Residue 333 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3rc7 Combined Structural and Functional Investigation of a C-3''-Ketoreductase Involved in the Biosynthesis of dTDP-l-Digitoxose.
Resolution2.0 Å
Binding residue
(original residue number in PDB)
G16 C17 A18 D19 I20 S42 R43 Y63 P78 L79 P80 H84 E101 K102 I169 R170 V175 D182
Binding residue
(residue number reindexed from 1)
G9 C10 A11 D12 I13 S35 R36 Y56 P71 L72 P73 H77 E94 K95 I162 R163 V168 D175
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) K102 F186
Catalytic site (residue number reindexed from 1) K95 F179
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:3rc7, PDBe:3rc7, PDBj:3rc7
PDBsum3rc7
PubMed21598943
UniProtB3TMR8|KIJDR_ACTKI dTDP-3,4-didehydro-2,6-dideoxy-alpha-D-glucose 3-reductase (Gene Name=KijD10)

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