4DM3

Crystal structure of human PNMT in complex adohcy, resorcinol and imidazole

• PDB DOI: https://doi.org/10.2210/pdb4DM3/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-02-06 Released: 2012-04-25 
• Deposition Author(s): Nair, P.C., Malde, A.K., Mark, A.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.275 
• R-Value Work: 0.220 
• R-Value Observed: 0.223 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 3KPY

Literature

Missing fragments: detecting cooperative binding in fragment-based drug design.

Nair, P.C., Malde, A.K., Drinkwater, N., Mark, A.E.

(2012) ACS Med Chem Lett 3: 322-326

• PubMed: 24900472 
• DOI: https://doi.org/10.1021/ml300015u
• Primary Citation of Related Structures:  
  4DM3


• PubMed Abstract: 
  

  The aim of fragment-based drug design (FBDD) is to identify molecular fragments that bind to alternate subsites within a given binding pocket leading to cooperative binding when linked. In this study, the binding of fragments to human phenylethanolamine N-methyltransferase is used to illustrate how (a) current protocols may fail to detect fragments that bind cooperatively, (b) theoretical approaches can be used to validate potential hits, and (c) apparent false positives obtained when screening against cocktails of fragments may in fact indicate promising leads.

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Organizational Affiliation: 

School of Chemistry and Molecular Biosciences (SCMB) and Institute for Molecular Bioscience (IMB), The University of Queensland (UQ) , St Lucia Campus, Brisbane, QLD 4072, Australia.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 64.82 kDa 
• Atom Count: 4,394 
• Modelled Residue Count: 525 
• Deposited Residue Count: 578 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylethanolamine N-methyltransferase	A, B	289	Homo sapiens	Mutation(s): 0  Gene Names: PNMT, PENT EC: 2.1.1.28
UniProt & NIH Common Fund Data Resources
Find proteins for P11086 (Homo sapiens) Explore P11086  Go to UniProtKB:  P11086
PHAROS:  P11086 GTEx:  ENSG00000141744

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	C [auth A], F [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
RCO	D [auth A], G [auth B]	RESORCINOL C6 H6 O2 GHMLBKRAJCXXBS-UHFFFAOYSA-N
IMD	E [auth A], H [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.275 
• R-Value Work: 0.220 
• R-Value Observed: 0.223 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.908	α = 90
b = 93.908	β = 90
c = 188.615	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-25 
Deposition Author(s): Nair, P.C., Malde, A.K., Mark, A.E.

Revision History  

• Version 1.0: 2012-04-25
  Type: Initial release
  
• Version 1.1: 2014-09-17
  Changes: Database references
• Version 1.2: 2018-01-24
  Changes: Advisory, Structure summary
• Version 1.3: 2024-11-27
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary