1YA4

Crystal Structure of Human Liver Carboxylesterase 1 in complex with tamoxifen

PDB DOI: https://doi.org/10.2210/pdb1YA4/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2004-12-17 Released: 2005-08-02
Deposition Author(s): Fleming, C.D., Bencharit, S., Edwards, C.C., Hyatt, J.L., Morton, C.L., Howard-Williams, E.L., Potter, P.M., Redinbo, M.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.252
R-Value Work: 0.203
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 180.41 kDa
Atom Count: 12,878
Modelled Residue Count: 1,595
Deposited Residue Count: 1,596
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CES1 protein	A, B, C	532	Homo sapiens	Mutation(s): 0 EC: 3.1.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P23141 (Homo sapiens) Explore P23141 Go to UniProtKB: P23141
PHAROS: P23141 GTEx: ENSG00000198848
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23141
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CTX Query on CTX Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain H [auth A] SDF format, chain O [auth B] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B]	H [auth A] I [auth A] N [auth B] O [auth B] T [auth C] H [auth A], I [auth A], N [auth B], O [auth B], T [auth C], U [auth C]	(Z)-2-[4-(1,2)-DIPHENYL-1-BUTENYL)-PHENOXY]-N,N-DIMETHYLETHANAMINE C₂₆ H₂₉ N O NKANXQFJJICGDU-QPLCGJKRSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain T [auth C] Focus chain U [auth C]
SIA Query on SIA Download Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain E [auth A] SDF format, chain K [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B]	E [auth A], K [auth B], Q [auth C]	N-acetyl-alpha-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-YRMXFSIDSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain Q [auth C] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain Q [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain P [auth C] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth C]	D [auth A], J [auth B], P [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain P [auth C] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain P [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain G [auth A] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B]	F [auth A] G [auth A] L [auth B] M [auth B] R [auth C] F [auth A], G [auth A], L [auth B], M [auth B], R [auth C], S [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
CTX	PDBBind: 1YA4	Ki: 1.52e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.252
R-Value Work: 0.203
R-Value Observed: 0.203
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.369	α = 90
b = 179.954	β = 90
c = 201.584	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-08-02

Deposition Author(s):

Howard-Williams, E.L.

Potter, P.M.

Redinbo, M.R.

Revision History (Full details and data files)

Version 1.0: 2005-08-02
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary
Version 1.4: 2023-08-23
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

1YA4

Crystal Structure of Human Liver Carboxylesterase 1 in complex with tamoxifen

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)