3U9W

Structure of human Leukotriene A4 hydrolase in complex with inhibitor sc57461A

PDB DOI: https://doi.org/10.2210/pdb3U9W/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-10-20 Released: 2012-10-24
Deposition Author(s): Niegowski, D., Thunnissen, M., Tholander, F., Rinaldo-Matthis, A., Muroya, A., Haeggstrom, J.Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.161
R-Value Work: 0.134
R-Value Observed: 0.134

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of human Leukotriene A4 hydrolase in complex with inhibitor sc57461A

Olsson, U., Niegowski, D., Stsiapanava, A., Thunnissen, M., Haeggstrom, J.Z., Rinaldo-Matthis, A.

To be published.

Macromolecule Content

Total Structure Weight: 71.21 kDa
Atom Count: 5,907
Modelled Residue Count: 608
Deposited Residue Count: 608
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leukotriene A-4 hydrolase	A	608	Homo sapiens	Mutation(s): 0 Gene Names: LTA4H, LTA4 EC: 3.3.2.6 (PDB Primary Data), 3.4.11.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P09960 (Homo sapiens) Explore P09960 Go to UniProtKB: P09960
PHAROS: P09960 GTEx: ENSG00000111144
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09960
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
28P Query on 28P Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	N-[3-(4-benzylphenoxy)propyl]-N-methyl-beta-alanine C₂₀ H₂₅ N O₃ HSXNVULMYZGNGF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
YB Query on YB Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain C [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain C [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A]	C [auth A] K [auth A] L [auth A] M [auth A] N [auth A] C [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	YTTERBIUM (III) ION Yb AWSFICBXMUKWSK-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain C [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain R [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain R [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain R [auth A]	F [auth A], G [auth A], R [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain R [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain R [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
28P	BindingDB: 3U9W	Ki: 3 (nM) from 1 assay(s)
		Kd: min: 60, max: 350 (nM) from 3 assay(s)
		IC50: min: 2.5, max: 49 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.161
R-Value Work: 0.134
R-Value Observed: 0.134
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.078	α = 90
b = 86.799	β = 90
c = 99.145	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
AUTOMAR	data collection

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-10-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-10-24
Type: Initial release
Version 1.1: 2018-03-07
Changes: Data collection
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations