Structure of PDB 1ep2 Chain A Binding Site BS01

Receptor Information

>1ep2 Chain A (length=305) Species: 1358 (Lactococcus lactis)

ENNRLSVKLPGLDLKNPIIPASGCFGFGEEYAKYYDLNKLGSIMVKATTL
HPRFGNPTPRVAETASGMLNAIGLQNPGLEVIMTEKLPWLNENFPELPII
ANVAGSEEADYVAVCAKIGDAANVKAIELNISCPNGQAFGTDPEVAAALV
KACKAVSKVPLYVKLSPNVTDIVPIAKAVEAAGADGLTMINTLMGVRFDL
KTRQPILANITGGLSGPAIKPVALKLIHQVAQDVDIPIIGMGGVANAQDV
LEMYMAGASAVAVGTANFADPFVCPKIIDKLPELMDQYRIESLESLIQEV
KEGKK

Ligand information

• Ligand ID: FMN
• InChI: InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
• InChIKey: FVTCRASFADXXNN-SCRDCRAPSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
  OpenEye OEToolkits 1.7.6: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
  ACDLabs 12.01: N=2C(=O)NC(=O)C3=Nc1cc(C)c(C)cc1N(C=23)CC(O)C(O)C(O)COP(=O)(O)O
  CACTVS 3.385: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C
  CACTVS 3.385: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C
• Formula: C17 H21 N4 O9 P
• Name: FLAVIN MONONUCLEOTIDE;
  RIBOFLAVIN MONOPHOSPHATE
• ChEMBL: CHEMBL1201794
• DrugBank: DB03247
• ZINC: ZINC000003831425
• PDB chain: 1ep2 Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1ep2 Structure of dihydroorotate dehydrogenase B: electron transfer between two flavin groups bridged by an iron-sulphur cluster.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): S24 G25 C26 K48 A49 N72 N104 N132 K170 N197 S221 G222 M247 G248 G249 G270 T271
• Binding residue (residue number reindexed from 1): S22 G23 C24 K46 A47 N70 N102 N130 K164 N191 S215 G216 M241 G242 G243 G264 T265
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): K48 N72 L76 C135 N137 K170 N197
• Catalytic site (residue number reindexed from 1): K46 N70 L74 C133 N135 K164 N191
• Enzyme Commision number: 1.3.1.14: dihydroorotate dehydrogenase (NAD(+)).

Gene Ontology

Molecular Function

• GO:0004152 dihydroorotate dehydrogenase activity
• GO:0004589 dihydroorotate dehydrogenase (NAD+) activity
• GO:0005515 protein binding
• GO:0016491 oxidoreductase activity
• GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors

Biological Process

• GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process
• GO:0006221 pyrimidine nucleotide biosynthetic process
• GO:0006222 UMP biosynthetic process
• GO:0044205 'de novo' UMP biosynthetic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:1ep2, PDBe:1ep2, PDBj:1ep2
• PDBsum: 1ep2
• PubMed: 11188687
• UniProt: P54322|PYRDB_LACLM Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit (Gene Name=pyrDB)