Structure of PDB 4c3y Chain D Binding Site BS01

Receptor Information
>4c3y Chain D (length=508) Species: 1833 (Rhodococcus erythropolis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DWTSECDVLVVGSGGGALTGAYTAAAQGLTTIVLEKTDRFGGTSAYSGAS
IWLPGTQVQERAGLPDSTENARTYLRALLGDAESERQDAYVETAPAVVAL
LEQNPNIEFEFRAFPDYYKAEGRMDTGRSINPLDLDPADIGDLAGKVRPE
LDQDRTGQDHAPGPMIGGRALIGRLLAAVQSTGKAELRTESVLTSLIVED
GRVVGAEVESGGETQRIKANRGVLMAAGGIEGNAEMREQAGTPGKAIWSM
GPFGANTGDAISAGIAVGGATALLDQAWFCPGVEQPDGSAAFMVGVRGGL
VVDSAGERYLNESLPYDQFGRAMDAHDDNGSAVPSFMIFDSREGGGLPAI
CIPNTAPAKHLEAGTWVGADTLEELAAKTGLPADALRSTVEKFNDAAKLG
VDEEFHRGEDPYDAFFCPPNGGANAALTAIENGPFYAARIVLSDLGTKGG
LVTDVNGRVLRADGSAIDGLYAAGNTSASLSGRFYPGPGVPLGTAMVFSY
RAAQDMAK
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain4c3y Chain D Residue 551 [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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PDB4c3y Crystal Structure and Site-Directed Mutagenesis of 3-Ketosteroid Delta1-Dehydrogenase from Rhodococcus Erythropolis Sq1 Explain its Catalytic Mechanism
Resolution2.3 Å
Binding residue
(original residue number in PDB)		G16 E37 K38 G44 T45 S46 S49 G50 S52 V194 L195 A229 G230 N258 D261 L447 N477 G491 P493 L494
Binding residue
(residue number reindexed from 1)		G14 E35 K36 G42 T43 S44 S47 G48 S50 V192 L193 A227 G228 N256 D259 L445 N475 G489 P491 L492
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C282 V296 R299 Y318 L447 G448 Y487
Catalytic site (residue number reindexed from 1) C280 V294 R297 Y316 L445 G446 Y485
Enzyme Commision number 1.3.99.4: 3-oxosteroid 1-dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016491 oxidoreductase activity
GO:0033765 steroid dehydrogenase activity, acting on the CH-CH group of donors
GO:0047571 3-oxosteroid 1-dehydrogenase activity
Biological Process
GO:0008202 steroid metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4c3y, PDBe:4c3y, PDBj:4c3y
PDBsum4c3y
PubMed24165124
UniProtQ9RA02

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