7GKK

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 JIN-POS-6dc588a4-6 (Mpro-P0906)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
QXR (Subject of Investigation/LOI)
Query on QXR

Download Ideal Coordinates CCD File 
J [auth A],
O [auth B]
N-(4-tert-butoxypyridin-3-yl)-2-(3-chlorophenyl)acetamide
C17 H19 Cl N2 O2
QOGVQOIEARJILE-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
K [auth A],
L [auth A],
M [auth B],
N [auth B],
P [auth B],
Q [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL
Query on CL

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.27α = 90
b = 99.04β = 90
c = 103.36γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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