7GIP

Group deposition SARS-CoV-2 main protease in complex with inhibitors from the COVID Moonshot -- Crystal Structure of SARS-CoV-2 main protease in complex with RAL-THA-8416115c-5 (Mpro-P0122)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted QI7Click on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors.

Boby, M.L.Fearon, D.Ferla, M.Filep, M.Koekemoer, L.Robinson, M.C.Chodera, J.D.Lee, A.A.London, N.von Delft, A.von Delft, F.Achdout, H.Aimon, A.Alonzi, D.S.Arbon, R.Aschenbrenner, J.C.Balcomb, B.H.Bar-David, E.Barr, H.Ben-Shmuel, A.Bennett, J.Bilenko, V.A.Borden, B.Boulet, P.Bowman, G.R.Brewitz, L.Brun, J.Bvnbs, S.Calmiano, M.Carbery, A.Carney, D.W.Cattermole, E.Chang, E.Chernyshenko, E.Clyde, A.Coffland, J.E.Cohen, G.Cole, J.C.Contini, A.Cox, L.Croll, T.I.Cvitkovic, M.De Jonghe, S.Dias, A.Donckers, K.Dotson, D.L.Douangamath, A.Duberstein, S.Dudgeon, T.Dunnett, L.E.Eastman, P.Erez, N.Eyermann, C.J.Fairhead, M.Fate, G.Fedorov, O.Fernandes, R.S.Ferrins, L.Foster, R.Foster, H.Fraisse, L.Gabizon, R.Garcia-Sastre, A.Gawriljuk, V.O.Gehrtz, P.Gileadi, C.Giroud, C.Glass, W.G.Glen, R.C.Glinert, I.Godoy, A.S.Gorichko, M.Gorrie-Stone, T.Griffen, E.J.Haneef, A.Hassell Hart, S.Heer, J.Henry, M.Hill, M.Horrell, S.Huang, Q.Y.J.Huliak, V.D.Hurley, M.F.D.Israely, T.Jajack, A.Jansen, J.Jnoff, E.Jochmans, D.John, T.Kaminow, B.Kang, L.Kantsadi, A.L.Kenny, P.W.Kiappes, J.L.Kinakh, S.O.Kovar, B.Krojer, T.La, V.N.T.Laghnimi-Hahn, S.Lefker, B.A.Levy, H.Lithgo, R.M.Logvinenko, I.G.Lukacik, P.Macdonald, H.B.MacLean, E.M.Makower, L.L.Malla, T.R.Marples, P.G.Matviiuk, T.McCorkindale, W.McGovern, B.L.Melamed, S.Melnykov, K.P.Michurin, O.Miesen, P.Mikolajek, H.Milne, B.F.Minh, D.Morris, A.Morris, G.M.Morwitzer, M.J.Moustakas, D.Mowbray, C.E.Nakamura, A.M.Neto, J.B.Neyts, J.Nguyen, L.Noske, G.D.Oleinikovas, V.Oliva, G.Overheul, G.J.Owen, C.D.Pai, R.Pan, J.Paran, N.Payne, A.M.Perry, B.Pingle, M.Pinjari, J.Politi, B.Powell, A.Psenak, V.Pulido, I.Puni, R.Rangel, V.L.Reddi, R.N.Rees, P.Reid, S.P.Reid, L.Resnick, E.Ripka, E.G.Robinson, R.P.Rodriguez-Guerra, J.Rosales, R.Rufa, D.A.Saar, K.Saikatendu, K.S.Salah, E.Schaller, D.Scheen, J.Schiffer, C.A.Schofield, C.J.Shafeev, M.Shaikh, A.Shaqra, A.M.Shi, J.Shurrush, K.Singh, S.Sittner, A.Sjo, P.Skyner, R.Smalley, A.Smeets, B.Smilova, M.D.Solmesky, L.J.Spencer, J.Strain-Damerell, C.Swamy, V.Tamir, H.Taylor, J.C.Tennant, R.E.Thompson, W.Thompson, A.Tomasio, S.Tomlinson, C.W.E.Tsurupa, I.S.Tumber, A.Vakonakis, I.van Rij, R.P.Vangeel, L.Varghese, F.S.Vaschetto, M.Vitner, E.B.Voelz, V.Volkamer, A.Walsh, M.A.Ward, W.Weatherall, C.Weiss, S.White, K.M.Wild, C.F.Witt, K.D.Wittmann, M.Wright, N.Yahalom-Ronen, Y.Yilmaz, N.K.Zaidmann, D.Zhang, I.Zidane, H.Zitzmann, N.Zvornicanin, S.N.

(2023) Science 382: eabo7201-eabo7201

  • DOI: https://doi.org/10.1126/science.abo7201
  • Primary Citation of Related Structures:  
    7GAV, 7GAW, 7GAX, 7GAY, 7GAZ, 7GB0, 7GB1, 7GB2, 7GB3, 7GB4, 7GB5, 7GB6, 7GB7, 7GB8, 7GB9, 7GBA, 7GBB, 7GBC, 7GBD, 7GBE, 7GBF, 7GBG, 7GBH, 7GBI, 7GBJ, 7GBK, 7GBL, 7GBM, 7GBN, 7GBO, 7GBP, 7GBQ, 7GBR, 7GBS, 7GBT, 7GBU, 7GBV, 7GBW, 7GBX, 7GBY, 7GBZ, 7GC0, 7GC1, 7GC2, 7GC3, 7GC4, 7GC5, 7GC6, 7GC7, 7GC8

  • PubMed Abstract: 

    We report the results of the COVID Moonshot, a fully open-science, crowdsourced, and structure-enabled drug discovery campaign targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease. We discovered a noncovalent, nonpeptidic inhibitor scaffold with lead-like properties that is differentiated from current main protease inhibitors. Our approach leveraged crowdsourcing, machine learning, exascale molecular simulations, and high-throughput structural biology and chemistry. We generated a detailed map of the structural plasticity of the SARS-CoV-2 main protease, extensive structure-activity relationships for multiple chemotypes, and a wealth of biochemical activity data. All compound designs (>18,000 designs), crystallographic data (>490 ligand-bound x-ray structures), assay data (>10,000 measurements), and synthesized molecules (>2400 compounds) for this campaign were shared rapidly and openly, creating a rich, open, and intellectual property-free knowledge base for future anticoronavirus drug discovery.


  • Organizational Affiliation

    Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase
A, B
306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QI7 (Subject of Investigation/LOI)
Query on QI7

Download Ideal Coordinates CCD File 
F [auth A],
N [auth B]
(4R)-6-chloro-1-[(1H-imidazol-2-yl)methyl]-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroquinoline-4-carboxamide
C23 H20 Cl N5 O
ALSINHANKODPSI-GOSISDBHSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
G [auth A]
H [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
Q [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.32α = 90
b = 98.77β = 90
c = 102.94γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted QI7Click on this verticalbar to view details

Entry History & Funding Information

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-08
    Type: Initial release
  • Version 1.1: 2023-12-06
    Changes: Author supporting evidence, Database references