1B6A

HUMAN METHIONINE AMINOPEPTIDASE 2 COMPLEXED WITH TNP-470

• PDB DOI: https://doi.org/10.2210/pdb1B6A/pdb

• Classification: ANGIOGENESIS INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda multiple nucleopolyhedrovirus
• Mutation(s): No 


• Deposited: 1999-01-13 Released: 2000-01-13 
• Deposition Author(s): Liu, S., Clardy, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.216 
• R-Value Work: 0.187 
• R-Value Observed: 0.187 

Starting Model: experimental

Literature

Structure of human methionine aminopeptidase-2 complexed with fumagillin.

Liu, S., Widom, J., Kemp, C.W., Crews, C.M., Clardy, J.

(1998) Science 282: 1324-1327

• PubMed: 9812898 
• DOI: https://doi.org/10.1126/science.282.5392.1324
• Primary Citation of Related Structures:  
  1B59, 1B6A, 1BN5, 1BOA


• PubMed Abstract: 
  

  The fungal metabolite fumagillin suppresses the formation of new blood vessels, and a fumagillin analog is currently in clinical trials as an anticancer agent. The molecular target of fumagillin is methionine aminopeptidase-2 (MetAP-2). A 1.8 A resolution crystal structure of free and inhibited human MetAP-2 shows a covalent bond formed between a reactive epoxide of fumagillin and histidine-231 in the active site of MetAP-2. Extensive hydrophobic and water-mediated polar interactions with other parts of fumagillin provide additional affinity. Fumagillin-based drugs inhibit MetAP-2 but not MetAP-1, and the three-dimensional structure also indicates the likely determinants of this specificity. The structural basis for fumagillin's potency and specificity forms the starting point for structure-based drug design.

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Organizational Affiliation: 

J. Clardy, Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, NY 14853-1301, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 53.49 kDa 
• Atom Count: 3,028 
• Modelled Residue Count: 355 
• Deposited Residue Count: 478 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METHIONINE AMINOPEPTIDASE	A	478	Homo sapiens	Mutation(s): 0  EC: 3.4.11.18
UniProt & NIH Common Fund Data Resources
Find proteins for P50579 (Homo sapiens) Go to UniProtKB:  P50579
PHAROS:  P50579 GTEx:  ENSG00000111142

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TN4	D [auth A]	(1R,2S,3S,4R)-4-hydroxy-2-methoxy-4-methyl-3-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]cyclohexyl (chloroacetyl)carbamate C19 H30 Cl N O6 OUUSPVSSNHLIGE-AGYLCKTBSA-N
CO	B [auth A], C [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TN4	BindingDB:  1B6A	Ki: 1 (nM) from 1 assay(s)
		IC50: min: 1, max: 1320 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.216 
• R-Value Work: 0.187 
• R-Value Observed: 0.187 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.558	α = 90
b = 99.06	β = 90
c = 101.508	γ = 90

Software Package:

Software Name	Purpose
SYNCHROTRON	data collection
SCALA	data scaling
CNS	refinement
SOFTWARE	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-01-13 
Deposition Author(s): Liu, S., Clardy, J.C.

Revision History  

• Version 1.0: 2000-01-13
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-08-31
  Changes: Non-polymer description
• Version 1.4: 2019-11-20
  Changes: Advisory, Derived calculations
• Version 1.5: 2023-08-02
  Changes: Database references, Derived calculations, Refinement description
• Version 1.6: 2024-10-23
  Changes: Data collection, Structure summary