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Literature DB >> 25050154

Protein-ligand cocrystal structures: we can do better.

Abstract

There is a large body of evidence that many protein-ligand cocrystal structures contain poorly refined ligand geometries. These errors result in bound structures that have nonideal bond lengths and angles, are strained, contain improbable conformations, and have bad protein-ligand contacts. Many of these problems can be greatly reduced with better refinement models.

Keywords: Protein−ligand cocrystal; bound ligand strain; structure refinement; structure-based design; structure-induced fit

Year: 2014 PMID： 25050154 PMCID： PMC4094245 DOI： 10.1021/ml500220a

Source DB: PubMed Journal: ACS Med Chem Lett ISSN： 1948-5875 Impact factor: 4.345

9 in total

Review 1. Application and limitations of X-ray crystallographic data in structure-based ligand and drug design.

Authors: Andrew M Davis; Simon J Teague; Gerard J Kleywegt
Journal: Angew Chem Int Ed Engl Date: 2003-06-23 Impact factor: 15.336

2. Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding.

Authors: Emanuele Perola; Paul S Charifson
Journal: J Med Chem Date: 2004-05-06 Impact factor: 7.446

3. PDB ligand conformational energies calculated quantum-mechanically.

Authors: Markus Sitzmann; Iwona E Weidlich; Igor V Filippov; Chenzhong Liao; Megan L Peach; Wolf-Dietrich Ihlenfeldt; Rajeshri G Karki; Yulia V Borodina; Raul E Cachau; Marc C Nicklaus
Journal: J Chem Inf Model Date: 2012-02-21 Impact factor: 4.956

4. Automated ligand placement and refinement with a combined force field and shape potential.

Authors: S Wlodek; A G Skillman; A Nicholls
Journal: Acta Crystallogr D Biol Crystallogr Date: 2006-06-20

5. Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package.

Authors: Oleg Y Borbulevych; Joshua A Plumley; Roger I Martin; Kenneth M Merz; Lance M Westerhoff
Journal: Acta Crystallogr D Biol Crystallogr Date: 2014-04-26

6. Conformational changes of small molecules binding to proteins.

Authors: M C Nicklaus; S Wang; J S Driscoll; G W Milne
Journal: Bioorg Med Chem Date: 1995-04 Impact factor: 3.641

7. Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.

Authors: Timothy D Fenn; Michael J Schnieders; Marat Mustyakimov; Chuanjie Wu; Paul Langan; Vijay S Pande; Axel T Brunger
Journal: Structure Date: 2011-04-13 Impact factor: 5.006

8. The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures.

Authors: John Liebeschuetz; Jana Hennemann; Tjelvar Olsson; Colin R Groom
Journal: J Comput Aided Mol Des Date: 2012-01-14 Impact factor: 3.686

9. Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX.

Authors: Jeffrey A Bell; Kenneth L Ho; Ramy Farid
Journal: Acta Crystallogr D Biol Crystallogr Date: 2012-07-17

9 in total

16 in total

1. Carbohydrate anomalies in the PDB.

Authors: Jon Agirre; Gideon Davies; Keith Wilson; Kevin Cowtan
Journal: Nat Chem Biol Date: 2015-05 Impact factor: 15.040

2. Molecular-interaction and signaling profiles of AM3677, a novel covalent agonist selective for the cannabinoid 1 receptor.

Authors: David R Janero; Suma Yaddanapudi; Nikolai Zvonok; Kumar V Subramanian; Vidyanand G Shukla; Edward Stahl; Lei Zhou; Dow Hurst; James Wager-Miller; Laura M Bohn; Patricia H Reggio; Ken Mackie; Alexandros Makriyannis
Journal: ACS Chem Neurosci Date: 2015-05-29 Impact factor: 4.418

3. When Does Chemical Elaboration Induce a Ligand To Change Its Binding Mode?

Authors: Shipra Malhotra; John Karanicolas
Journal: J Med Chem Date: 2016-12-16 Impact factor: 7.446

4. Conformational investigation of the structure-activity relationship of GdFFD and its analogues on an achatin-like neuropeptide receptor of Aplysia californica involved in the feeding circuit.

Authors: Thanh D Do; James W Checco; Michael Tro; Joan-Emma Shea; Michael T Bowers; Jonathan V Sweedler
Journal: Phys Chem Chem Phys Date: 2018-08-29 Impact factor: 3.676

Review 5. Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding.

Authors: Megan L Peach; Raul E Cachau; Marc C Nicklaus
Journal: J Mol Recognit Date: 2017-02-24 Impact factor: 2.137

6. Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality.

Authors: Gydo C P van Zundert; Nigel W Moriarty; Oleg V Sobolev; Paul D Adams; Kenneth W Borrelli
Journal: Structure Date: 2021-04-05 Impact factor: 5.871

7. Targeting human central nervous system protein kinases: An isoform selective p38αMAPK inhibitor that attenuates disease progression in Alzheimer's disease mouse models.

Authors: Saktimayee M Roy; Valerie L Grum-Tokars; James P Schavocky; Faisal Saeed; Agnieszka Staniszewski; Andrew F Teich; Ottavio Arancio; Adam D Bachstetter; Scott J Webster; Linda J Van Eldik; George Minasov; Wayne F Anderson; Jeffrey C Pelletier; D Martin Watterson
Journal: ACS Chem Neurosci Date: 2015-02-23 Impact factor: 4.418