3Q2G | pdb_00003q2g

Adamts1 in complex with a novel N-hydroxyformamide inhibitors

PDB DOI: https://doi.org/10.2210/pdb3Q2G/pdb

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

Deposited: 2010-12-20 Released: 2011-03-30
Deposition Author(s): Gerhardt, S., Hargreaves, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.261 (Depositor), 0.268 (DCC)
R-Value Work:
0.208 (Depositor), 0.218 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The design and synthesis of novel N-hydroxyformamide inhibitors of ADAM-TS4 for the treatment of osteoarthritis

De Savi, C., Pape, A., Cumming, J.G., Ting, A., Smith, P.D., Burrows, J.N., Mills, M., Davies, C., Lamont, S., Milne, D., Cook, C., Moore, P., Sawyer, Y., Gerhardt, S.

(2011) Bioorg Med Chem Lett 21: 1376-1381

PubMed: 21300546 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2011.01.036
Primary Citation Related Structures:
3Q2G, 3Q2H

PubMed Abstract:
Two series of N-hydroxyformamide inhibitors of ADAM-TS4 were identified from screening compounds previously synthesised as inhibitors of matrix metalloproteinase-13 (collagenase-3). Understanding of the binding mode of this class of compound using ADAM-TS1 as a structural surrogate has led to the discovery of potent and very selective inhibitors with favourable DMPK properties. Synthesis, structure-activity relationships, and strategies to improve selectivity and lower in vivo metabolic clearance are described.

Organizational Affiliation

Respiratory and Inflammation Research Area, AstraZeneca, Alderley Park, Macclesfield, Cheshire, UK. chris.desavi2@astrazeneca.com

Macromolecule Content

Total Structure Weight: 67.85 kDa
Atom Count: 4,572
Modeled Residue Count: 564
Deposited Residue Count: 594
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
A disintegrin and metalloproteinase with thrombospondin motifs 1	A, B	297	Homo sapiens	Mutation(s): 0 Gene Names: ADAMTS1 EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHI8 (Homo sapiens) Explore Q9UHI8 Go to UniProtKB: Q9UHI8
PHAROS: Q9UHI8 GTEx: ENSG00000154734
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UHI8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QGF Query on QGF Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain C [auth A] MOL2 format, chain R [auth B] MOL2 format, chain C [auth A] mmCIF format, chain R [auth B] mmCIF format, chain C [auth A]	C [auth A], R [auth B]	N-[(2S,4S)-1-({4-[(2,4-dichlorobenzyl)oxy]piperidin-1-yl}sulfonyl)-4-(5-fluoropyrimidin-2-yl)-2-methylpentan-2-yl]-N-hydroxyformamide C₂₃ H₂₉ Cl₂ F N₄ O₅ S YSYXAGMNRKARQB-HJPURHCSSA-N		Interactions Focus chain C [auth A] Focus chain R [auth B] Interactions & Density Focus chain C [auth A] Focus chain R [auth B]
CD Query on CD Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain V [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain V [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], H [auth A], I [auth A], V [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain V [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain V [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain D [auth A] MOL2 format, chain S [auth B] MOL2 format, chain D [auth A] mmCIF format, chain S [auth B] mmCIF format, chain D [auth A]	D [auth A], S [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain S [auth B] Interactions & Density Focus chain D [auth A] Focus chain S [auth B]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain G [auth A] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain G [auth A] mmCIF format, chain AA [auth B]	AA [auth B] G [auth A] J [auth A] K [auth A] L [auth A] AA [auth B], G [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], T [auth B], U [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain G [auth A] Focus chain J [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 T [auth B] Focus chain U [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain G [auth A] Focus chain J [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 T [auth B] Focus chain U [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.261 (Depositor), 0.268 (DCC)
R-Value Work: 0.208 (Depositor), 0.218 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.309	α = 90
b = 63.419	β = 89.88
c = 114.912	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-03-30

Deposition Author(s):

Gerhardt, S.

Hargreaves, D.

Revision History (Full details and data files)

Version 1.0: 2011-03-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-06
Changes: Structure summary