7FY9 | pdb_00007fy9

Crystal Structure of human FABP4 binding site mutated to that of FABP5 in complex with 2-cyclopentyl-4-(4-fluorophenyl)-6-[1-(methoxymethyl)cyclopentyl]-3-methyl-5-(1H-tetrazol-5-yl)pyridine, i.e. SMILES c1(c(nc(c(c1c1ccc(cc1)F)C1=NN=NN1)C1(CCCC1)COC)C1CCCC1)C with IC50=0.14164 microM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 
    0.275 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: other
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

A high-resolution data set of fatty acid-binding protein structures. III. Unexpectedly high occurrence of wrong ligands.

Ehler, A.Bartelmus, C.Benz, J.Plitzko, I.Rudolph, M.G.

(2025) Acta Crystallogr D Struct Biol 81: 451-464


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fatty acid-binding protein, adipocyte135Homo sapiensMutation(s): 8 
Gene Names: FABP4
UniProt & NIH Common Fund Data Resources
Find proteins for P15090 (Homo sapiens)
Explore P15090 
Go to UniProtKB:  P15090
PHAROS:  P15090
GTEx:  ENSG00000170323 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15090
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K7C (Subject of Investigation/LOI)
Query on K7C

Download Ideal Coordinates CCD File 
B [auth A](5P)-2-cyclopentyl-4-(4-fluorophenyl)-6-[1-(methoxymethyl)cyclopentyl]-3-methyl-5-(1H-tetrazol-5-yl)pyridine
C25 H30 F N5 O
LIYRSWZUQWQZTJ-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
C [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free:  0.275 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.672α = 90
b = 53.455β = 90
c = 72.409γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
F. Hoffmann-La Roche LTDSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Structure summary
  • Version 1.3: 2025-08-13
    Changes: Database references