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Structure paper

TitleStructure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.
Journal, issue, pagesNat Commun, Vol. 12, Page 4848-4848, Year 2021
Publish dateSep 16, 2020 (structure data deposition date)
AuthorsNewman, J.A. / Douangamath, A. / Yadzani, S. / Yosaatmadja, Y. / Aimon, A. / Brandao-Neto, J. / Dunnett, L. / Gorrie-Stone, T. / Skyner, R. / Fearon, D. ...Newman, J.A. / Douangamath, A. / Yadzani, S. / Yosaatmadja, Y. / Aimon, A. / Brandao-Neto, J. / Dunnett, L. / Gorrie-Stone, T. / Skyner, R. / Fearon, D. / Schapira, M. / von Delft, F. / Gileadi, O.
External linksNat Commun / PubMed:34381037
MethodsX-ray diffraction
Resolution1.788 - 3.04 Å
Structure data

PDB-5rl6:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z198195770
Method: X-RAY DIFFRACTION / Resolution: 1.921 Å

PDB-5rl7:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z364321922
Method: X-RAY DIFFRACTION / Resolution: 1.89 Å

PDB-5rl8:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z53825177
Method: X-RAY DIFFRACTION / Resolution: 2.21 Å

PDB-5rl9:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1703168683
Method: X-RAY DIFFRACTION / Resolution: 1.788 Å

PDB-5rlb:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z216450634
Method: X-RAY DIFFRACTION / Resolution: 1.98 Å

PDB-5rlc:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z56923284
Method: X-RAY DIFFRACTION / Resolution: 1.92 Å

PDB-5rld:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z19735981
Method: X-RAY DIFFRACTION / Resolution: 2.233 Å

PDB-5rle:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1429867185
Method: X-RAY DIFFRACTION / Resolution: 2.268 Å

PDB-5rlf:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z235341991
Method: X-RAY DIFFRACTION / Resolution: 2.235 Å

PDB-5rlg:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z19739650
Method: X-RAY DIFFRACTION / Resolution: 1.96 Å

PDB-5rlh:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z2856434778
Method: X-RAY DIFFRACTION / Resolution: 2.379 Å

PDB-5rli:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z45617795
Method: X-RAY DIFFRACTION / Resolution: 2.26 Å

PDB-5rlj:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1407673036
Method: X-RAY DIFFRACTION / Resolution: 1.879 Å

PDB-5rlk:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1509882419
Method: X-RAY DIFFRACTION / Resolution: 1.956 Å

PDB-5rll:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z425387594
Method: X-RAY DIFFRACTION / Resolution: 2.08 Å

PDB-5rlm:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1650168321
Method: X-RAY DIFFRACTION / Resolution: 1.858 Å

PDB-5rln:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z364328788
Method: X-RAY DIFFRACTION / Resolution: 2.147 Å

PDB-5rlo:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1454310449
Method: X-RAY DIFFRACTION / Resolution: 2.097 Å

PDB-5rlp:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z166605480
Method: X-RAY DIFFRACTION / Resolution: 2.562 Å

PDB-5rlq:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z285782452
Method: X-RAY DIFFRACTION / Resolution: 2.225 Å

PDB-5rlr:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z822382694
Method: X-RAY DIFFRACTION / Resolution: 2.32 Å

PDB-5rls:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z59181945
Method: X-RAY DIFFRACTION / Resolution: 2.278 Å

PDB-5rlt:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z53116498
Method: X-RAY DIFFRACTION / Resolution: 2.43 Å

PDB-5rlu:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z744754722
Method: X-RAY DIFFRACTION / Resolution: 2.347 Å

PDB-5rlv:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z2467208649
Method: X-RAY DIFFRACTION / Resolution: 2.21 Å

PDB-5rlw:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z45705015
Method: X-RAY DIFFRACTION / Resolution: 1.97 Å

PDB-5rly:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z2027049478
Method: X-RAY DIFFRACTION / Resolution: 2.434 Å

PDB-5rlz:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z2293643386
Method: X-RAY DIFFRACTION / Resolution: 1.97 Å

PDB-5rm0:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1492796719
Method: X-RAY DIFFRACTION / Resolution: 1.909 Å

PDB-5rm1:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z426041412
Method: X-RAY DIFFRACTION / Resolution: 1.896 Å

PDB-5rm2:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1741964527
Method: X-RAY DIFFRACTION / Resolution: 1.82 Å

PDB-5rm3:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1745658474
Method: X-RAY DIFFRACTION / Resolution: 2.09 Å

PDB-5rm4:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1639162606
Method: X-RAY DIFFRACTION / Resolution: 2.96 Å

PDB-5rm5:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z373768900
Method: X-RAY DIFFRACTION / Resolution: 2.06 Å

PDB-5rm6:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z396380540
Method: X-RAY DIFFRACTION / Resolution: 2.128 Å

PDB-5rm7:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z69118333
Method: X-RAY DIFFRACTION / Resolution: 1.84 Å

PDB-5rm8:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1614545742
Method: X-RAY DIFFRACTION / Resolution: 2.143 Å

PDB-5rm9:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z2856434942
Method: X-RAY DIFFRACTION / Resolution: 2.076 Å

PDB-5rma:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z321318226
Method: X-RAY DIFFRACTION / Resolution: 1.89 Å

PDB-5rmb:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z2856434920
Method: X-RAY DIFFRACTION / Resolution: 2.206 Å

PDB-5rmc:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z24758179
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

PDB-5rmd:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z57614330
Method: X-RAY DIFFRACTION / Resolution: 1.92 Å

PDB-5rme:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z26333434
Method: X-RAY DIFFRACTION / Resolution: 2.23 Å

PDB-5rmf:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z54226006
Method: X-RAY DIFFRACTION / Resolution: 2.23 Å

PDB-5rmg:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z285675722
Method: X-RAY DIFFRACTION / Resolution: 2.115 Å

PDB-5rmh:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1101755952
Method: X-RAY DIFFRACTION / Resolution: 2.021 Å

PDB-5rmi:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z53860899
Method: X-RAY DIFFRACTION / Resolution: 2.116 Å

PDB-5rmj:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z68299550
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-5rmk:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1273312153
Method: X-RAY DIFFRACTION / Resolution: 2.08 Å

PDB-5rml:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z85956652
Method: X-RAY DIFFRACTION / Resolution: 2.43 Å

PDB-5rmm:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with POB0066
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-6zsl:
Crystal structure of the SARS-CoV-2 helicase at 1.94 Angstrom resolution
Method: X-RAY DIFFRACTION / Resolution: 1.94 Å

PDB-7nio:
Crystal structure of the SARS-CoV-2 helicase APO form
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-7nn0:
Crystal structure of the SARS-CoV-2 helicase in complex with AMP-PNP
Method: X-RAY DIFFRACTION / Resolution: 3.04 Å

PDB-7nng:
Crystal structure of the SARS-CoV-2 helicase in complex with Z2327226104
Method: X-RAY DIFFRACTION / Resolution: 2.38 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-PO4:
PHOSPHATE ION / Phosphate

ChemComp-LJA:
N-[3-(carbamoylamino)phenyl]acetamide

ChemComp-HOH:
WATER / Water

ChemComp-VVD:
5-(acetylamino)-2-fluorobenzoic acid

ChemComp-VVG:
N-(2-fluorophenyl)ethanesulfonamide

ChemComp-UR7:
1-(3-fluoro-4-methylphenyl)methanesulfonamide

ChemComp-VVJ:
N-cycloheptyl-N-methylmethanesulfonamide

ChemComp-VVM:
4-amino-N-phenylbenzene-1-sulfonamide

ChemComp-VVY:
2-phenoxy-1-(pyrrolidin-1-yl)ethan-1-one

ChemComp-VVP:
4-methoxy-1H-indole

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

ChemComp-VW1:
(2S)-2-(4-cyanophenoxy)propanamide

ChemComp-K2P:
2-(trifluoromethoxy)benzoic acid

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

ChemComp-VW4:
(2S)-2-phenylpropane-1-sulfonamide

ChemComp-NYV:
1-(propan-2-yl)-1H-imidazole-4-sulfonamide

ChemComp-H04:
1-(2-ethoxyphenyl)piperazine

ChemComp-VW7:
N-(8-methyl-1,2,3,4-tetrahydroquinolin-5-yl)acetamide

ChemComp-NZG:
3-(acetylamino)-4-fluorobenzoic acid

ChemComp-UQS:
N-[(2-fluorophenyl)methyl]-1H-pyrazol-4-amine

ChemComp-VWA:
(1S)-1-(4-fluorophenyl)-N-methylethan-1-amine

ChemComp-UVA:
N-methyl-2-(methylsulfonyl)aniline

ChemComp-VWD:
(1R)-2-(methylsulfonyl)-1-phenylethan-1-ol

ChemComp-VWG:
N-hydroxyquinoline-2-carboxamide

ChemComp-UVJ:
3-(2-methyl-1H-benzimidazol-1-yl)propanamide

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

ChemComp-VWJ:
N-(propan-2-yl)-1H-benzimidazol-2-amine

ChemComp-S9S:
~{N}-[2-(4-fluorophenyl)ethyl]methanesulfonamide

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

ChemComp-VWM:
(3R)-1-acetyl-3-hydroxypiperidine-3-carboxylic acid

ChemComp-S7G:
~{N}-[(3~{R})-1,2,3,4-tetrahydroquinolin-3-yl]ethanamide

ChemComp-RY4:
N-[4-(aminomethyl)phenyl]methanesulfonamide

ChemComp-UXG:
1-(diphenylmethyl)azetidin-3-ol

ChemComp-S7J:
2-(trifluoromethyl)pyrimidine-5-carboxamide

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

ChemComp-NUA:
N-(1-ethyl-1H-pyrazol-4-yl)cyclobutanecarboxamide

ChemComp-HR5:
~{N}-(cyclobutylmethyl)-1,5-dimethyl-pyrazole-4-carboxamide

ChemComp-N0E:
~{N}-(4-hydroxyphenyl)-3-phenyl-propanamide

ChemComp-GQJ:
methyl (2~{S},4~{R})-1-(furan-2-ylcarbonyl)-4-oxidanyl-pyrrolidine-2-carboxylate

ChemComp-EJQ:
~{N}-(4-fluorophenyl)-2-pyrrolidin-1-yl-ethanamide

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

ChemComp-VWV:
ethyl (1,1-dioxo-1lambda~6~,4-thiazinan-4-yl)acetate

ChemComp-6SU:
methyl 3-(methylsulfonylamino)benzoate

ChemComp-VWY:
N-ethyl-4-[(methylsulfonyl)amino]benzamide

ChemComp-RYM:
4-(benzimidazol-1-ylmethyl)benzenecarbonitrile

ChemComp-NX7:
(2,6-difluorophenyl)(pyrrolidin-1-yl)methanone

ChemComp-MUK:
4,6-dimethyl-~{N}-phenyl-pyrimidin-2-amine / Pyrimethanil

ChemComp-VX4:
[(4S)-4-methylazepan-1-yl](1,3-thiazol-4-yl)methanone

ChemComp-STV:
~{N}-(1,3-benzodioxol-5-ylmethyl)ethanesulfonamide

ChemComp-JOV:
3-chloro-N-(1-hydroxy-2-methylpropan-2-yl)benzamide

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

ChemComp-VXD:
N-(3-chloro-2-methylphenyl)glycinamide

ChemComp-VXG:
(3S,4R)-1-acetyl-4-phenylpyrrolidine-3-carboxylic acid

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

ChemComp-UJK:
1-(2-methylphenyl)-1,2,3-triazole-4-carboxylic acid

Source
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / HYDROLASE / SARS-CoV-2 Helicase NSP13 / NSP13 / Helicase / SARS-CoV-2

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