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TitleGroup deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD)
Journal, issue, pagesTo Be Published
Publish dateAug 11, 2025 (structure data deposition date)
AuthorsLuptak, J. / Aschenbrenner, J.C. / Balcomb, B.H. / Marples, P.G. / Bellini, D. / Yu, C.W. / Douangamath, A. / Dias, A. / Powell, A. / Fearon, D. ...Luptak, J. / Aschenbrenner, J.C. / Balcomb, B.H. / Marples, P.G. / Bellini, D. / Yu, C.W. / Douangamath, A. / Dias, A. / Powell, A. / Fearon, D. / James, L. / von Delft, F.
External linksSearch PubMed
MethodsX-ray diffraction
Resolution1.52 - 1.86 Å
Structure data

PDB-7ilm:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z2472938267 (Nprot-x0072)
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-7iln:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z2856434879 (Nprot-x0083)
Method: X-RAY DIFFRACTION / Resolution: 1.73 Å

PDB-7ilo:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z1416571195 (Nprot-x0084)
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7ilp:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z275151340 (Nprot-x0098)
Method: X-RAY DIFFRACTION / Resolution: 1.64 Å

PDB-7ilq:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z44592329 (Nprot-x0125)
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-7ilr:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z321318226 (Nprot-x0138)
Method: X-RAY DIFFRACTION / Resolution: 1.54 Å

PDB-7ils:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z2443429438 (Nprot-x0180)
Method: X-RAY DIFFRACTION / Resolution: 1.67 Å

PDB-7ilt:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z1545313172 (Nprot-x0190)
Method: X-RAY DIFFRACTION / Resolution: 1.72 Å

PDB-7ilu:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z2234920345 (Nprot-x0220)
Method: X-RAY DIFFRACTION / Resolution: 1.62 Å

PDB-7ilv:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z31385861 (Nprot-x0230)
Method: X-RAY DIFFRACTION / Resolution: 1.54 Å

PDB-7ilw:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z907784200 (Nprot-x0249)
Method: X-RAY DIFFRACTION / Resolution: 1.56 Å

PDB-7ilx:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z1259341037 (Nprot-x0263)
Method: X-RAY DIFFRACTION / Resolution: 1.54 Å

PDB-7ily:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z56837087 (Nprot-x0275)
Method: X-RAY DIFFRACTION / Resolution: 1.62 Å

PDB-7ilz:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z1673618163 (Nprot-x0300)
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-7im0:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z56791867 (Nprot-x0303)
Method: X-RAY DIFFRACTION / Resolution: 1.59 Å

PDB-7im1:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z57472297 (Nprot-x0318)
Method: X-RAY DIFFRACTION / Resolution: 1.68 Å

PDB-7im2:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z319545618 (Nprot-x0329)
Method: X-RAY DIFFRACTION / Resolution: 1.62 Å

PDB-7im3:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z1273312153 (Nprot-x0334)
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-7im4:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z969560582 (Nprot-x0340)
Method: X-RAY DIFFRACTION / Resolution: 1.61 Å

PDB-7im5:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z45527714 (Nprot-x0343)
Method: X-RAY DIFFRACTION / Resolution: 1.76 Å

PDB-7im6:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z26781964 (Nprot-x0345)
Method: X-RAY DIFFRACTION / Resolution: 1.57 Å

PDB-7im7:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z29077827 (Nprot-x0358)
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-7im8:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z31478538 (Nprot-x0359)
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-7im9:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z19733482 (Nprot-x0361)
Method: X-RAY DIFFRACTION / Resolution: 1.79 Å

PDB-7ima:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z1563512128 (Nprot-x0369)
Method: X-RAY DIFFRACTION / Resolution: 1.64 Å

PDB-7imb:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z235341991 (Nprot-x0372)
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-7imc:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z2856434779 (Nprot-x0374)
Method: X-RAY DIFFRACTION / Resolution: 1.54 Å

PDB-7imd:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z453319206 (Nprot-x0385)
Method: X-RAY DIFFRACTION / Resolution: 1.63 Å

PDB-7ime:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z1407672867 (Nprot-x0389)
Method: X-RAY DIFFRACTION / Resolution: 1.63 Å

PDB-7imf:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z2697514548 (Nprot-x0390)
Method: X-RAY DIFFRACTION / Resolution: 1.56 Å

PDB-7img:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z1267882044 (Nprot-x0392)
Method: X-RAY DIFFRACTION / Resolution: 1.68 Å

PDB-7imh:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z45617795 (Nprot-x0395)
Method: X-RAY DIFFRACTION / Resolution: 1.69 Å

PDB-7imi:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z1407673036 (Nprot-x0401)
Method: X-RAY DIFFRACTION / Resolution: 1.54 Å

PDB-7imj:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z2527301677 (Nprot-x0403)
Method: X-RAY DIFFRACTION / Resolution: 1.64 Å

PDB-7imk:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z1270312110 (Nprot-x0412)
Method: X-RAY DIFFRACTION / Resolution: 1.54 Å

PDB-7iml:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z1220452176 (Nprot-x0423)
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-7imm:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z166605480 (Nprot-x0438)
Method: X-RAY DIFFRACTION / Resolution: 1.77 Å

PDB-7imn:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z744754722 (Nprot-x0467)
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-7imo:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z68404778 (Nprot-x0477)
Method: X-RAY DIFFRACTION / Resolution: 1.72 Å

PDB-7imp:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z805551440 (Nprot-x0483)
Method: X-RAY DIFFRACTION / Resolution: 1.52 Å

PDB-7imq:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z2027049478 (Nprot-x0488)
Method: X-RAY DIFFRACTION / Resolution: 1.53 Å

PDB-7imr:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z1954800564 (Nprot-x0525)
Method: X-RAY DIFFRACTION / Resolution: 1.53 Å

PDB-7ims:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z165170770 (Nprot-x0540)
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-7imt:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z1639162606 (Nprot-x0543)
Method: X-RAY DIFFRACTION / Resolution: 1.86 Å

PDB-7imu:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z198195774 (Nprot-x0552)
Method: X-RAY DIFFRACTION / Resolution: 1.71 Å

PDB-7imv:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z33546965 (Nprot-x0556)
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-7imw:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z28870646 (Nprot-x0615)
Method: X-RAY DIFFRACTION / Resolution: 1.69 Å

PDB-7imx:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z1359419878 (Nprot-x0616)
Method: X-RAY DIFFRACTION / Resolution: 1.58 Å

PDB-7imy:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z2204875953 (Nprot-x0642)
Method: X-RAY DIFFRACTION / Resolution: 1.77 Å

PDB-7imz:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z1530301542 (Nprot-x0648)
Method: X-RAY DIFFRACTION / Resolution: 1.72 Å

PDB-7in0:
Group deposition for crystallographic fragment screening of SARS-CoV-2 nucleocapsid protein (CTD) -- Crystal Structure of SARS-CoV-2 nucleocapsid protein (CTD) in complex with Z102768020 (Nprot-x0656)
Method: X-RAY DIFFRACTION / Resolution: 1.68 Å

Chemicals

ChemComp-S6V:
1-[2-(2-oxidanylidenepyrrolidin-1-yl)ethyl]-3-phenyl-urea

ChemComp-IPA:
ISOPROPYL ALCOHOL

ChemComp-HOH:
WATER

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-2L1:
2-[(4-methyl-1H-imidazol-5-yl)methyl]-1,2,3,4-tetrahydroisoquinoline

ChemComp-WZ7:
2-[(cyclopent-3-en-1-yl)amino]pyridine-4-carboxamide

ChemComp-JHP:
4-chloro-N-cyclopentyl-1-methyl-1H-pyrazole-3-carboxamide

ChemComp-DMS:
DIMETHYL SULFOXIDE / DMSO, precipitant*YM

ChemComp-K0G:
N-phenyl-N'-pyridin-3-ylurea

ChemComp-JHJ:
N-(4-methoxyphenyl)-N'-pyridin-4-ylurea

ChemComp-WNM:
(3S)-1-(phenylsulfonyl)pyrrolidin-3-amine

ChemComp-LWA:
(2~{S})-~{N}-(4-aminocarbonylphenyl)oxolane-2-carboxamide

ChemComp-VZS:
N-(2-methoxy-5-methylphenyl)-N'-4H-1,2,4-triazol-4-ylurea

ChemComp-GUG:
~{N}-propan-2-ylquinoline-2-carboxamide

PDB-1cnc:
COMPENSATORY PLASTIC EFFECTS IN THE REDESIGN OF PROTEIN-ZINC BINDING SITES

ChemComp-WH4:
N-(propan-2-yl)pyridin-3-amine

ChemComp-ELN:
~{N}-(4-chlorophenyl)-2-cyano-ethanamide

ChemComp-WL7:
4-amino-N-(2-hydroxyethyl)-N-methylbenzene-1-sulfonamide

ChemComp-K1S:
N,N-diethyl-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-amine

ChemComp-AYV:
1-[2-methyl-1,3-bis(oxidanyl)propan-2-yl]-3-phenyl-urea

ChemComp-RXS:
3-[(2-methyl-1H-imidazol-1-yl)methyl]benzonitrile

ChemComp-CL:
Unknown entry

ChemComp-O2A:
N-methyl-1H-indole-7-carboxamide

ChemComp-GOL:
GLYCEROL

ChemComp-K24:
N,2-dimethyl-1,3-thiazole-5-carboxamide

ChemComp-X0S:
2-chloro-N-methylbenzene-1-sulfonamide

ChemComp-W0D:
N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide

ChemComp-GTJ:
~{N}-(1-propylbenzimidazol-2-yl)propanamide

ChemComp-T9Q:
N-Benzyl-2-methoxyacetamide

PDB-1and:
ANIONIC TRYPSIN MUTANT WITH ARG 96 REPLACED BY HIS

ChemComp-M0J:
N-[(2S)-2-hydroxypropyl]-N'-phenylurea

ChemComp-NY7:
N-(2-methoxy-5-methylphenyl)glycinamide

ChemComp-BP4:
biphenyl-4-ylacetic acid / antiinflammatory*YM

ChemComp-LWD:
~{N}-quinolin-6-ylbenzamide

ChemComp-GWP:
2-cyclopropyl-1~{H}-imidazole-4-carboxamide

ChemComp-GWG:
1-methylindazole-3-carboxamide


PDB Unreleased entry

PDB-1bfl: Unknown entry

ChemComp-JFM:
N-(2-phenylethyl)methanesulfonamide

PDB-1a32:
RIBOSOMAL PROTEIN S15 FROM BACILLUS STEAROTHERMOPHILUS

PDB-1aj5:
CALPAIN DOMAIN VI APO

ChemComp-K31:
2-(3,5-dimethyl-1H-pyrazol-4-yl)aniline

ChemComp-HWH:
~{N}-[2-(5-fluoranyl-1~{H}-indol-3-yl)ethyl]ethanamide

PDB-1cnb:
COMPENSATORY PLASTIC EFFECTS IN THE REDESIGN OF PROTEIN-ZINC BINDING SITES

ChemComp-JG4:
2-(thiophen-2-yl)-1H-imidazole

ChemComp-B1A:
~{N}-(4-phenylazanylphenyl)ethanamide

PDB-1h9v:
Human Fc-gamma-Receptor IIa (FcgRIIa), monoclinic

ChemComp-K34:
5-(1,3-thiazol-2-yl)-1H-1,2,4-triazole

ChemComp-NZ1:
5-methoxy-1,3-benzothiazol-2-amine

ChemComp-W0Y:
N-methyl-4-sulfamoylbenzamide

ChemComp-PK4:
2-fluoro-N,3-dimethylbenzene-1-sulfonamide

PDB-1cne:
STRUCTURAL STUDIES ON CORN NITRATE REDUCTASE: REFINED STRUCTURE OF THE CYTOCHROME B REDUCTASE FRAGMENT AT 2.5 ANGSTROMS, ITS ADP COMPLEX AND AN ACTIVE SITE MUTANT AND MODELING OF THE CYTOCHROME B DOMAIN

ChemComp-ONQ:
~{N}-(2-azanyl-2-oxidanylidene-ethyl)-4-methoxy-benzamide

ChemComp-TVP:
(2S)-1-ACETYL-2-METHYL-1,2,3,4-TETRAHYDROQUINOLINE


ChemComp, No image

ChemComp-K6U:
Unknown entry

ChemComp-Q7L:
(3P)-3-(2H-1,3-benzodioxol-5-yl)-1H-pyrazole

ChemComp-ZQA:
4-ethyl-2-(1H-imidazol-5-yl)-1,3-thiazole

ChemComp-W1Y:
N-methyl-1-(1-phenyl-1H-pyrazol-4-yl)methanamine

Source
  • severe acute respiratory syndrome coronavirus 2
  • sars-cov-2 (virus)
KeywordsVIRAL PROTEIN / Diamond I04-1 / PanDDA2 / XChemExplorer / crystallographic fragment screening / SARS-CoV-2 / nucleocapsid protein / N protein

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