Structure of PDB 5mgb Chain B Binding Site BS01

Receptor Information

>5mgb Chain B (length=720) Species: 10116 (Rattus norvegicus)

SHMAEYLRLPHSLAMIRLCNPPVNAVSPTVIREVRNGLQKAGSDHTVKAI
VICGANGNFCAGADIHGFSAFTPGLALGSLVDEIQRYQKPVLAAIQGVAL
GGGLELALGCHYRIANAKARVGLPEVTLGILPGARGTQLLPRVVGVPVAL
DLITSGKYLSADEALRLGILDAVVKSDPVEEAIKFAQKIIDKPIEPRRIF
NKPVPSLPNMDSVFAEAIAKVRKQYPGVLAPETCVRSIQASVKHPYEVGI
KEEEKLFMYLRASGQAKALQYAFFAEKSANKWSTPSGASWKTASAQPVSS
VGVLGLGTMGRGIAISFARVGISVVAVESDPKQLDAAKKIITFTLEKEAS
RAHQNGQASAKPKLRFSSSTKELSTVDLVVEAVFEDMNLKKKVFAELSAL
CKPGAFLCTNTSALNVDDIASSTDRPQLVIGTHFFSPAHVMRLLEVIPSR
YSSPTTIATVMSLSKKIGKIGVVVGNCYGFVGNRMLAPYYNQGFFLLEEG
SKPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIRKGQGLTGPSLPPGTP
VRKRGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDPWLSTF
LSQYREVHHIEQRTISKEEILERCLYSLINEAFRILEEGMAARPEHIDVI
YLHGYGWPRHKGGPMFYAASVGLPTVLEKLQKYYRQNPDIPQLEPSDYLR
RLVAQGSPPLKEWQSLAGPH

Ligand information

• Ligand ID: CAA
• InChI: InChI=1S/C25H40N7O18P3S/c1-13(33)8-16(35)54-7-6-27-15(34)4-5-28-23(38)20(37)25(2,3)10-47-53(44,45)50-52(42,43)46-9-14-19(49-51(39,40)41)18(36)24(48-14)32-12-31-17-21(26)29-11-30-22(17)32/h11-12,14,18-20,24,36-37H,4-10H2,1-3H3,(H,27,34)(H,28,38)(H,42,43)(H,44,45)(H2,26,29,30)(H2,39,40,41)/t14-,18-,19-,20+,24-/m1/s1
• InChIKey: OJFDKHTZOUZBOS-CITAKDKDSA-N
• SMILES:
  CACTVS 3.341: CC(=O)CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
  CACTVS 3.341: CC(=O)CC(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 1.5.0: CC(=O)CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
  OpenEye OEToolkits 1.5.0: CC(=O)CC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
  ACDLabs 10.04: O=C(C)CC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
• Formula: C25 H40 N7 O18 P3 S
• Name: ACETOACETYL-COENZYME A
• DrugBank: DB03059
• ZINC: ZINC000096014521
• PDB chain: 5mgb Chain B Residue 802

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5mgb Structural enzymology comparisons of multifunctional enzyme, type-1 (MFE1): the flexibility of its dehydrogenase part.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): P20 V21 A59 G60 A61 D62 I63 F66 G100 P122 E123 L126 Y156 K275
• Binding residue (residue number reindexed from 1): P22 V23 A61 G62 A63 D64 I65 F68 G102 P124 E125 L128 Y158 K277
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): A61 F66 G76 G100 E103 P122 E123 P130 G131 K249 S410 H431 E443 N481
• Catalytic site (residue number reindexed from 1): A63 F68 G78 G102 E105 P124 E125 P132 G133 K251 S412 H433 E445 N483
• Enzyme Commision number: 1.1.1.35: 3-hydroxyacyl-CoA dehydrogenase.
  4.2.1.17: enoyl-CoA hydratase.
  5.3.3.8: Delta(3)-Delta(2)-enoyl-CoA isomerase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0003857 3-hydroxyacyl-CoA dehydrogenase activity
• GO:0004165 delta(3)-delta(2)-enoyl-CoA isomerase activity
• GO:0004300 enoyl-CoA hydratase activity
• GO:0016491 oxidoreductase activity
• GO:0016509 long-chain-3-hydroxyacyl-CoA dehydrogenase activity
• GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
• GO:0016829 lyase activity
• GO:0016853 isomerase activity
• GO:0016863 intramolecular oxidoreductase activity, transposing C=C bonds
• GO:0019899 enzyme binding
• GO:0070403 NAD+ binding

Biological Process

• GO:0006631 fatty acid metabolic process
• GO:0006635 fatty acid beta-oxidation

Cellular Component

• GO:0005777 peroxisome
• GO:0005829 cytosol

External links

• PDB: RCSB:5mgb, PDBe:5mgb, PDBj:5mgb
• PDBsum: 5mgb
• PubMed: 29226071
• UniProt: P07896|ECHP_RAT Peroxisomal bifunctional enzyme (Gene Name=Ehhadh)