3LU6 | pdb_00003lu6

Human serum albumin in complex with compound 1

PDB DOI: https://doi.org/10.2210/pdb3LU6/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2010-02-17 Released: 2010-10-27
Deposition Author(s): Buttar, D., Colclough, N., Gerhardt, S., MacFaul, P.A., Phillips, S.D., Plowright, A., Whittamore, P., Tam, K., Maskos, K., Steinbacher, S., Steuber, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.275 (Depositor), 0.277 (DCC)
R-Value Work:
0.236 (Depositor), 0.235 (DCC)
R-Value Observed:
0.238 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

A combined spectroscopic and crystallographic approach to probing drug-human serum albumin interactions

Buttar, D., Colclough, N., Gerhardt, S., Macfaul, P.A., Phillips, S.D., Plowright, A., Whittamore, P., Tam, K., Maskos, K., Steinbacher, S., Steuber, H.

(2010) Bioorg Med Chem 18: 7486-7496

PubMed: 20869876 Search on PubMed
DOI: https://doi.org/10.1016/j.bmc.2010.08.052
Primary Citation Related Structures:
3LU6, 3LU7, 3LU8

PubMed Abstract:
The displacement of probes that bind selectively to subdomains IIA or IIIA on human serum albumin (HSA) by competing compounds has been followed using fluorescence spectroscopy, and has therefore been used to assign a primary binding site for these compounds in the presence and absence of fatty acids. The crystal structures have also been solved for three compounds: a matched pair of carboxylic acids whose binding strength to HSA unexpectedly decreased as the lipophilicity increased; and a highly bound sulphonamide that appeared not to displace the probes in the displacement assay. The crystallography results support the findings from the fluorescence displacement assay. The results indicate that drug binding to subdomain IB might also be important location for certain compounds.

Organizational Affiliation

AstraZeneca, Alderley Park, Macclesfield, Cheshire SK104TG, England, United Kingdom.

Macromolecule Content

Total Structure Weight: 134.55 kDa
Atom Count: 9,322
Modeled Residue Count: 1,156
Deposited Residue Count: 1,170
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serum albumin	A, B	585	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02768 (Homo sapiens) Explore P02768 Go to UniProtKB: P02768
PHAROS: P02768 GTEx: ENSG00000163631
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02768
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IMX Query on IMX Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth B], F [auth B]	[(1R,2R)-2-{[(5-fluoro-1H-indol-2-yl)carbonyl]amino}-2,3-dihydro-1H-inden-1-yl]acetic acid C₂₀ H₁₇ F N₂ O₃ MUKIEMZDXOXEOK-NVXWUHKLSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.275 (Depositor), 0.277 (DCC)
R-Value Work: 0.236 (Depositor), 0.235 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.561	α = 74.51
b = 59.868	β = 86.57
c = 95.573	γ = 74.47

Software Package:

Software Name	Purpose
MOSFLM	data reduction
MOLREP	phasing
REFMAC	refinement
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-10-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-10-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary