1OJA

HUMAN MONOAMINE OXIDASE B IN COMPLEX WITH ISATIN

PDB DOI: 10.2210/pdb1OJA/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Komagataella pastoris
Mutation(s): No
Membrane Protein: Yes PDBTMmpstruc

Deposited: 2003-07-08 Released: 2003-08-15
Deposition Author(s): Binda, C., Edmondson, D.E., Mattevi, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.204
R-Value Work: 0.181
R-Value Observed: 0.182

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Insights Into the Mode of Inhibition of Human Mitochondrial Monoamine Oxidase B from High-Resolution Crystal Structures

Binda, C., Li, M., Hubalek, F., Restelli, N., Edmondson, D.E., Mattevi, A.

(2003) Proc Natl Acad Sci U S A 100: 9750

PubMed: 12913124 Search on PubMedSearch on PubMed Central
DOI: 10.1073/pnas.1633804100
Primary Citation of Related Structures:
1OJ9, 1OJA, 1OJC, 1OJD

PubMed Abstract:

Monoamine oxidase B (MAO-B) is an outer mitochondrial membrane-bound enzyme that catalyzes the oxidative deamination of arylalkylamine neurotransmitters and has been a target for a number of clinically used drug inhibitors. The 1.7-A structure of the reversible isatin-MAO-B complex has been determined; it forms a basis for the interpretation of the enzyme's structure when bound to either reversible or irreversible inhibitors. 1,4-Diphenyl-2-butene is found to be a reversible MAO-B inhibitor, which occupies both the entrance and substrate cavity space in the enzyme. Comparison of these two structures identifies Ile-199 as a "gate" between the two cavities. Rotation of the side chain allows for either separation or fusion of the two cavities. Inhibition of the enzyme with N-(2-aminoethyl)-p-chlorobenzamide results in the formation of a covalent N(5) flavin adduct with the phenyl ring of the inhibitor occupying a position in the catalytic site overlapping that of isatin. Inhibition of MAO-B with the clinically used trans-2-phenylcyclopropylamine results in the formation of a covalent C(4a) flavin adduct with an opened cyclopropyl ring and the phenyl ring in a parallel orientation to the flavin. The peptide bond between the flavin-substituted Cys-397 and Tyr-398 is in a cis conformation, which allows the proper orientation of the phenolic ring of Tyr-398 in the active site. The flavin ring exists in a twisted nonplanar conformation, which is observed in the oxidized form as well as in both the N(5) and the C(4a) adducts. An immobile water molecule is H-bonded to Lys-296 and to the N(5) of the flavin as observed in other flavin-dependent amine oxidases. The active site cavities are highly apolar; however, hydrophilic areas exist near the flavin and direct the amine moiety of the substrate for binding and catalysis. Small conformational changes are observed on comparison of the different inhibitor-enzyme complexes. Future MAO-B drug design will need to consider "induced fit" contributions as an element in ligand-enzyme interactions.

Organizational Affiliation:

Department of Genetics and Microbiology, University of Pavia, Via Abbiategrasso, 27100 Pavia, Italy.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AMINE OXIDASE [FLAVIN-CONTAINING] B	A, B	520	Homo sapiens	Mutation(s): 0 Gene Names: MAOB EC: 1.4.3.4 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P27338 (Homo sapiens) Explore P27338 Go to UniProtKB: P27338
PHAROS: P27338 GTEx: ENSG00000069535
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P27338
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Ligand Interaction
ISN Query on ISN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	ISATIN C₈ H₅ N O₂ JXDYKVIHCLTXOP-UHFFFAOYSA-N		Ligand Interaction

Binding Affinity Annotations
ID	Source	Binding Affinity
ISN	BindingDB: 1OJA	Ki: min: 33, max: 6000 (nM) from 6 assay(s)
	BindingDB: 1OJA	IC50: min: 7943, max: 3.68e+5 (nM) from 7 assay(s)
	Binding MOAD: 1OJA	Ki: 3000 (nM) from 1 assay(s)