4FLK

Human MetAP1 with bengamide analog Y10, in Mn form

• PDB DOI: https://doi.org/10.2210/pdb4FLK/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-06-14 Released: 2012-09-19 
• Deposition Author(s): Ye, Q.Z., Xu, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.221 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 

Literature

Structural analysis of bengamide derivatives as inhibitors of methionine aminopeptidases.

Xu, W., Lu, J.P., Ye, Q.Z.

(2012) J Med Chem 55: 8021-8027

• PubMed: 22913487 
• DOI: https://doi.org/10.1021/jm3008695
• Primary Citation of Related Structures:  
  4FLI, 4FLJ, 4FLK, 4FLL


• PubMed Abstract: 
  

  Natural-product-derived bengamides possess potent antiproliferative activity and target human methionine aminopeptidases (MetAPs) for their cellular effects. Several derivatives were designed, synthesized, and evaluated as MetAP inhibitors. Here, we present four new X-ray structures of human MetAP1 in complex with the inhibitors. Together with the previous structures of bengamide derivatives with human MetAP2 and tubercular MtMetAP1c, analysis of the interactions of these inhibitors at the active site provides structural basis for further modification of these bengamide inhibitors for improved potency and selectivity as anticancer and antibacterial therapeutics.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.36 kDa 
• Atom Count: 2,599 
• Modelled Residue Count: 304 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine aminopeptidase 1	A	326	Homo sapiens	Mutation(s): 0  Gene Names: KIAA0094, map1, METAP1 EC: 3.4.11.18
UniProt & NIH Common Fund Data Resources
Find proteins for P53582 (Homo sapiens) Go to UniProtKB:  P53582
PHAROS:  P53582 GTEx:  ENSG00000164024

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y10	D [auth A]	(E,2R,3R,4S,5R)-N-(2,3-dihydro-1H-inden-2-yl)-2-methoxy-8,8-dimethyl-3,4,5-tris(oxidanyl)non-6-enamide C21 H31 N O5 XTHOIFAGDPGJPZ-PQQJDVFMSA-N
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
Y10	PDBBind:  4FLK	IC50: 5580 (nM) from 1 assay(s)
	BindingDB:  4FLK	IC50: 5580 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.221 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.777	α = 90
b = 77.506	β = 90.43
c = 48.62	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-19 
Deposition Author(s): Ye, Q.Z., Xu, W.

Revision History  

• Version 1.0: 2012-09-19
  Type: Initial release
  
• Version 1.1: 2012-11-14
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations