Structure of PDB 2bf4 Chain B Binding Site BS01

Receptor Information

>2bf4 Chain B (length=645) Species: 4932 (Saccharomyces cerevisiae)

NRDIAQVVTENNKNYLVLYASQTGTAEDYAKKFSKELVAKFNLNVMCADV
ENYDFESLNDVPVIVSIFISTYGEGDFPDGAVNFEDFICNAEAGALSNLR
YNMFGLGNSTYEFFNGAAKKAEKHLSAAGAIRLGKLGEADDGAGTTDEDY
MAWKDSILEVLKDELHLDEQEAKFTSQFQYTVLNEITDSMSLGEPSAHYL
PSHQLNRNADGIQLGPFDLSQPYIAPIVKSRELFSSNDRNCIHSEFDLSG
SNIKYSTGDHLAVWPSNPLEKVEQFLSIFNLDPETIFDLKPLDPTVKVPF
PTPTTIGAAIKHYLEITGPVSRQLFSSLIQFAPNADVKEKLTLLSKDKDQ
FAVEITSKYFNIADALKYLSDGAKWDTVPMQFLVESVPQMTPRYYSISSS
SLSEKQTVHVTSIVENFPNPELPDAPPVVGVTTNLLRNIQLAQNNVNIAE
TNLPVHYDLNGPRKLFANYKLPVHVRRSNFRLPSNPSTPVIMIGPGTGVA
PFRGFIRERVAFLESQKKGGNNVSLGKHILFYGSRNTDDFLYQDEWPEYA
KKLDGSFEMVVAHSRLPNTKKVYVQDKLKDYEDQVFEMINNGAFIYVCGD
AKGMAKGVSTALVGILSRGKSITTDEATELIKMLKTSGRYQEDVW

Ligand information

• Ligand ID: FAD
• InChI: InChI=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
• InChIKey: VWWQXMAJTJZDQX-UYBVJOGSSA-N
• SMILES:
  CACTVS 3.341: Cc1cc2N=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 1.5.0: Cc1cc2c(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 1.5.0: Cc1cc2c(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 3.341: Cc1cc2N=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 10.04: O=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
• Formula: C27 H33 N9 O15 P2
• Name: FLAVIN-ADENINE DINUCLEOTIDE
• ChEMBL: CHEMBL1232653
• DrugBank: DB03147
• ZINC: ZINC000008215434
• PDB chain: 2bf4 Chain B Residue 750

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2bf4 A Second Fmn-Binding Site in Yeast Nadph-Cytochrome P450 Reductase Suggests a Mechanism of Electron Transfer by Diflavin Reductases.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): H306 G364 P365 Y405 R439 Y440 Y441 S442 I459 E461 V474 V475 G476 V477 T478 T479 W691
• Binding residue (residue number reindexed from 1): H260 G318 P319 Y359 R393 Y394 Y395 S396 I413 E415 V428 V429 G430 V431 T432 T433 W645
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): Y441 S442 C644 D689 W691
• Catalytic site (residue number reindexed from 1): Y395 S396 C598 D643 W645
• Enzyme Commision number: 1.6.2.4: NADPH--hemoprotein reductase.

Gene Ontology

Molecular Function

• GO:0003958 NADPH-hemoprotein reductase activity
• GO:0003959 NADPH dehydrogenase activity
• GO:0009055 electron transfer activity
• GO:0010181 FMN binding
• GO:0016491 oxidoreductase activity
• GO:0050660 flavin adenine dinucleotide binding
• GO:0050661 NADP binding

Biological Process

• GO:0006696 ergosterol biosynthetic process
• GO:0016126 sterol biosynthetic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005741 mitochondrial outer membrane
• GO:0005783 endoplasmic reticulum
• GO:0005789 endoplasmic reticulum membrane
• GO:0005829 cytosol
• GO:0005886 plasma membrane

External links

• PDB: RCSB:2bf4, PDBe:2bf4, PDBj:2bf4
• PDBsum: 2bf4
• PubMed: 16407065
• UniProt: P16603|NCPR_YEAST NADPH--cytochrome P450 reductase (Gene Name=NCP1)