Structure of PDB 6dek Chain A Binding Site BS01

Receptor Information

>6dek Chain A (length=595) Species: 237561 (Candida albicans SC5314)

KKEQLMDDSFIGLTGGEIFHEMMLRHKVDTVFGYAGGAILPVFDAIYNSD
KFKFVLPRHEQGAGHMAEGYARASGKPGVVLVTSGPGATNVITPMADALM
DGVPLVVFSGQVPTTAIQEADIVGISRSCTKWNVMVKNVAELPRRINEAF
EIATTGRPGPVLVDLPKDVTASILRESIPINTTLPSNAVSEFTSEAIKRA
ANILNKAKKPIIYAGAGILNNEQGPKLLKELADKANIPVTTTLQGLGAFD
QRDPKSLDMLGMHGSAAANTAIQNADCIIALGARFDDRVTGNISKFAPEA
KLAASEGRGGILHFEISPKNINKVVEATEAIEGDVTANLQSFIPLVDSIE
NRPEWFNKINEWKKKYPYSYQLETPGSLIKPQTLIKEISDQAQTYNKEVI
VTTGVGQHQMWAAQHFTWTQPRTMITSGGLGTMGYGLPAAIGAQVAKPDA
IVIDIDGDASFNMTLTELSSAVQAGAPIKVCVLNNEEQGMVTQWQSLFYE
HRYSHTHQSNPDFMKLAESMNVKGIRITNQQELKSGVKEFLDATEPVLLE
VIVEKKVPVLPMVPAGKALDDFILWDAEVEKQQNDLRKERTGGKY

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: 6dek Chain A Residue 701

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6dek Commercial AHAS-inhibiting herbicides are promising drug leads for the treatment of human fungal pathogenic infections.
• Resolution: 2.971 Å
• Binding residue (original residue number in PDB): R237 G303 A304 G305 N308 T330 L331 Q332 L348 M350 G370 A371 R372 D374 R376 V377 E403 I404 N408 D422 V423 M498 G516
• Binding residue (residue number reindexed from 1): R157 G215 A216 G217 N220 T242 L243 Q244 L260 M262 G282 A283 R284 D286 R288 V289 E315 I316 N320 D334 V335 M410 G428
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): Y109 G111 G112 A113 I114 E135 T158 Q198 E199 K247 K314 M350 V377 V493 L518 G519 M521 D546 N573 E575 Q576 M578 V579 W582 L604 N609 V610
• Catalytic site (residue number reindexed from 1): Y34 G36 G37 A38 I39 E60 T83 Q118 E119 K167 K226 M262 V289 V405 L430 G431 M433 D458 N485 E487 Q488 M490 V491 W494 L516 N521 V522
• Enzyme Commision number: 2.2.1.6: acetolactate synthase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0000287 magnesium ion binding
• GO:0003824 catalytic activity
• GO:0003984 acetolactate synthase activity
• GO:0016740 transferase activity
• GO:0030976 thiamine pyrophosphate binding
• GO:0046872 metal ion binding
• GO:0050660 flavin adenine dinucleotide binding

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006412 translation
• GO:0008652 amino acid biosynthetic process
• GO:0009082 branched-chain amino acid biosynthetic process
• GO:0009097 isoleucine biosynthetic process
• GO:0009099 L-valine biosynthetic process
• GO:0030150 protein import into mitochondrial matrix

Cellular Component

• GO:0005948 acetolactate synthase complex

External links

• PDB: RCSB:6dek, PDBe:6dek, PDBj:6dek
• PDBsum: 6dek
• PubMed: 30249642
• UniProt: A0A1D8PJF9