4KC1 | pdb_00004kc1

Structure of the blood group glycosyltransferase AAglyB in complex with a pyridine inhibitor as a neutral pyrophosphate surrogate

PDB DOI: https://doi.org/10.2210/pdb4KC1/pdb

Classification: Transferase/Transferase Inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-04-24 Released: 2013-09-11
Deposition Author(s): Cuesta-Seijo, J.A., Wang, S., Lafont, D., Vidal, S., Palcic, M.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.180 (Depositor), 0.182 (DCC)
R-Value Work:
0.141 (Depositor), 0.140 (DCC)
R-Value Observed:
0.142 (Depositor)

Starting Model: experimental
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Literature

Design of glycosyltransferase inhibitors: pyridine as a pyrophosphate surrogate.

Wang, S., Cuesta-Seijo, J.A., Lafont, D., Palcic, M.M., Vidal, S.

(2013) Chemistry 19: 15346-15357

PubMed: 24108680 Search on PubMed
DOI: https://doi.org/10.1002/chem.201301871
Primary Citation Related Structures:
4KC1, 4KC2, 4KC4

PubMed Abstract:
A series of ten glycosyltransferase inhibitors has been designed and synthesized by using pyridine as a pyrophosphate surrogate. The series was prepared by conjugation of carbohydrate, pyridine, and nucleoside building blocks by using a combination of glycosylation, the Staudinger-Vilarrasa amide-bond formation, and azide-alkyne click chemistry. The compounds were evaluated as inhibitors of five metal-dependent galactosyltransferases. Crystallographic analyses of three inhibitors complexed in the active site of one of the enzymes confirmed that the pyridine moiety chelates the Mn(2+) ion causing a slight displacement (2 Å) from its original position. The carbohydrate head group occupies a different position than in the natural uridine diphosphate (UDP)-Gal substrate with little interaction with the enzyme.

Organizational Affiliation

Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Laboratoire de Chimie Organique 2, Glycochimie, UMR 5246, CNRS and Université Claude Bernard Lyon 1, 43 Boulevard du 11 Novembre 1918, 6922 Villeurbanne (France), Fax: (+33) 472-448-109.

Macromolecule Content

Total Structure Weight: 34.77 kDa
Atom Count: 2,992
Modeled Residue Count: 289
Deposited Residue Count: 290
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase	A	290	Homo sapiens	Mutation(s): 0 Gene Names: ABO EC: 2.4.1.40 (PDB Primary Data), 2.4.1.37 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P16442 (Homo sapiens) Explore P16442 Go to UniProtKB: P16442
PHAROS: P16442
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16442
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WS1 Query on WS1 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	6-(1-beta-D-Glucopyranosyloxymethyl)-N-(5'-deoxyluridine-5'-yl)picolinamide C₂₂ H₂₈ N₄ O₁₂ KPOTWZYLDCHCIG-MJELCBSSSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
BHE Query on BHE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	octyl 2-O-(6-deoxy-alpha-L-galactopyranosyl)-beta-D-galactopyranoside C₂₀ H₃₈ O₁₀ GTTDTLMUWQMDNA-ARNYJBIMSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MN Query on MN 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]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.180 (Depositor), 0.182 (DCC)
R-Value Work: 0.141 (Depositor), 0.140 (DCC)
R-Value Observed: 0.142 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.85	α = 90
b = 149.87	β = 90
c = 80	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-09-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-09-11
Type: Initial release
Version 1.1: 2015-03-04
Changes: Database references
Version 1.2: 2017-11-15
Changes: Advisory, Refinement description
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description