7FZV | pdb_00007fzv

Crystal Structure of human FABP4 in complex with 1-[(2,4-dichlorophenyl)methyl]-4-hydroxy-3-[(E)-3-phenylprop-2-enyl]pyridin-2-one, i.e. SMILES C1(=C(C=CN(C1=O)Cc1c(cc(cc1)Cl)Cl)O)C/C=C/c1ccccc1 with IC50=0.557 microM

PDB DOI: https://doi.org/10.2210/pdb7FZV/pdb
Deposition Group: G_1002264 | Explore G_1002264

Classification: LIPID BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-04-27 Released: 2023-06-14
Deposition Author(s): Ehler, A., Benz, J., Obst, U., Brunner, M., Rudolph, M.G.
Funding Organization(s): F. Hoffmann-La Roche LTD

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free:
0.252 (Depositor), 0.218 (DCC)
R-Value Work:
0.195 (Depositor)
R-Value Observed:
0.198 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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

PubMed: 40748031 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2059798325006096
Primary Citation Related Structures:
7FVU, 7FVV, 7FVW, 7FVX, 7FVY, 7FVZ, 7FW0, 7FW1, 7FW2, 7FW3, 7FW4, 7FW5, 7FW6, 7FW7, 7FW8, 7FW9, 7FWA, 7FWB, 7FWC, 7FWD, 7FWE, 7FWF, 7FWG, 7FWH, 7FWI, 7FWJ, 7FWK, 7FWL, 7FWM, 7FWN, 7FWO, 7FWP, 7FWQ, 7FWR, 7FWS, 7FWT, 7FWU, 7FWV, 7FWW, 7FWX, 7FWY, 7FWZ, 7FX0, 7FX1, 7FX2, 7FX3, 7FX4, 7FX5, 7FX6, 7FX7, ... Search all related entries

PubMed Abstract:
FABP4 has been implicated as a therapeutic target for treating diabetes and atherosclerosis. Structure-based drug design (SBDD) based on initial hits from high-throughput and fragment screens yielded 216 ligand-bound structures of human FABP3, FABP4 and FABP5 isoforms, many of which were at resolutions of better than 1.2 Å. An estimated 15% of the ligands had a different chemical composition to that expected from the starting materials or the final synthesis product, highlighting a potential problem inherent to all SBDD campaigns conducted at lower resolution. Apart from possible human error during compound registration, side reactions such as additions, eliminations, isomerizations, cyclizations and dimerizations were found that led to compounds capable of binding to FABP.

Organizational Affiliation

Therapeutic Modalities, Innovation Center Basel, F. Hoffmann-La Roche, Grenzacherstrasse 124, 4070 Basel, Switzerland.

Macromolecule Content

Total Structure Weight: 31.39 kDa
Atom Count: 2,188
Modeled Residue Count: 270
Deposited Residue Count: 270
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid-binding protein, adipocyte	A, B	135	Homo sapiens	Mutation(s): 0 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15090
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
O1L (Subject of Investigation/LOI) Query on O1L Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	E [auth A], J [auth B]	1-[(2,4-dichlorophenyl)methyl]-4-hydroxy-3-[(2E)-3-phenylprop-2-en-1-yl]pyridin-2(1H)-one C₂₁ H₁₇ Cl₂ N O₂ WFRAUCNBSDLATB-QPJJXVBHSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	C [auth A] D [auth A] F [auth B] G [auth B] H [auth B] C [auth A], D [auth A], F [auth B], G [auth B], H [auth B], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]