3C-like proteinase nsp5 (3CL-PRO) | P0DTD1 PRO_0000449623

Structure
Assessment

Oligo-State

Ligands

GMQE

QMEANDisCo Global

Homo-dimer (matching prediction)

2 x T8J

0.97

0.90 ± 0.05

2 x 1-[4-(thiophene-2-carbonyl)piperazin-1-yl]ethan-1-one

T8J.4:	11 residues within 4Å: Chain A: T.25, H.41, C.44, T.45, S.46, M.49, N.142, G.143, S.144, C.145, H.163 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.25 Hydrogen bonds: A:G.143, A:S.144, A:C.145
T8J.8:	11 residues within 4Å: Chain B: T.25, H.41, C.44, T.45, S.46, M.49, N.142, G.143, S.144, C.145, H.163 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:T.25 Hydrogen bonds: B:G.143, B:S.144, B:C.145

QMEANDisCo Local

QMEAN Z-Scores

Template	Seq Identity	Coverage	Description
5rfv.1.B	100.00%		3C-like proteinase PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102306

Ligand	Added to Model	Description
T8J	✓	1-[4-(thiophene-2-carbonyl)pi…
T8J	✓	1-[4-(thiophene-2-carbonyl)pi…
DMS	✕ - Not biologically relevant.	DIMETHYL SULFOXIDE
DMS	✕ - Not biologically relevant.	DIMETHYL SULFOXIDE
DMS	✕ - Not biologically relevant.	DIMETHYL SULFOXIDE
DMS	✕ - Not biologically relevant.	DIMETHYL SULFOXIDE
DMS	✕ - Not biologically relevant.	DIMETHYL SULFOXIDE
DMS	✕ - Not biologically relevant.	DIMETHYL SULFOXIDE

Model-Template Alignment

Structure
Assessment

Oligo-State

Ligands

GMQE

QMEANDisCo Global

Homo-dimer (matching prediction)

2 x HWH

0.97

0.90 ± 0.05

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

HWH.4:	11 residues within 4Å: Chain A: H.41, M.49, H.164, M.165, E.166, L.167, P.168, D.187, R.188, Q.189, T.190 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:M.165, A:Q.189 Hydrogen bonds: A:E.166 pi-Stacking: A:H.41
HWH.9:	11 residues within 4Å: Chain B: H.41, M.49, H.164, M.165, E.166, L.167, P.168, D.187, R.188, Q.189, T.190 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:M.165, B:Q.189 Hydrogen bonds: B:E.166 pi-Stacking: B:H.41

QMEANDisCo Local

QMEAN Z-Scores

Template	Seq Identity	Coverage	Description
5r7z.1.B	100.00%		3C-like proteinase PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1220452176

Ligand	Added to Model	Description
HWH	✓	~{N}-[2-(5-fluoranyl-1~{H}-in…
HWH	✓	~{N}-[2-(5-fluoranyl-1~{H}-in…
DMS	✕ - Not biologically relevant.	DIMETHYL SULFOXIDE
DMS	✕ - Not biologically relevant.	DIMETHYL SULFOXIDE
DMS	✕ - Not biologically relevant.	DIMETHYL SULFOXIDE
DMS	✕ - Not biologically relevant.	DIMETHYL SULFOXIDE
DMS	✕ - Not biologically relevant.	DIMETHYL SULFOXIDE
DMS	✕ - Not biologically relevant.	DIMETHYL SULFOXIDE
DMS	✕ - Not biologically relevant.	DIMETHYL SULFOXIDE
DMS	✕ - Not biologically relevant.	DIMETHYL SULFOXIDE

Model-Template Alignment

Structure
Assessment

Oligo-State	Ligands	GMQE	QMEANDisCo Global
Homo-dimer (matching prediction)	None	0.96	0.88 ± 0.05

QMEANDisCo Local

QMEAN Z-Scores

Template	Seq Identity	Coverage	Description
6lu7.1.B	100.00%		3C-like proteinase The crystal structure of COVID-19 main protease in complex with an inhibitor N3

Ligand	Added to Model	Description
02J-ALA-VAL-LEU-PJE-010	✕ - Clashing with protein.	N-[(5-METHYLISOXAZOL-3-YL)CAR…
02J-ALA-VAL-LEU-PJE-010	✕ - Clashing with protein.	N-[(5-METHYLISOXAZOL-3-YL)CAR…

Model-Template Alignment

Structure
Assessment

Oligo-State

Ligands

GMQE

QMEANDisCo Global

Homo-dimer (matching prediction)

2 x DTZ

0.95

0.88 ± 0.05

QMEANDisCo Local

QMEAN Z-Scores

Template	Seq Identity	Coverage	Description
2z9j.1.A	96.08%		3C-like proteinase Complex structure of SARS-CoV 3C-like protease with EPDTC

Ligand	Added to Model	Description
DTZ	✓	ZINC(II)HYDROGENSULFIDE
DTZ	✓	ZINC(II)HYDROGENSULFIDE
DMS	✕ - Not biologically relevant.	DIMETHYL SULFOXIDE
DMS	✕ - Not biologically relevant.	DIMETHYL SULFOXIDE
DMS	✕ - Not biologically relevant.	DIMETHYL SULFOXIDE
DMS	✕ - Not biologically relevant.	DIMETHYL SULFOXIDE

Model-Template Alignment

Template	Seq Identity	Coverage	Description
6y2g.1.A	100.00%		3C-like proteinase Crystal structure (orthorhombic form) of the complex resulting from the reaction between SARS-CoV-2 (2019-nCoV) main protease and tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate (alpha-ketoamide 13b)

Ligand	Added to Model	Description
GLY	✓	GLYCINE
O6K	✓	~{tert}-butyl ~{N}-[1-[(2~{S}…
O6K	✓	~{tert}-butyl ~{N}-[1-[(2~{S}…

Structure
Assessment

Oligo-State

Ligands

GMQE

QMEANDisCo Global

Homo-dimer (matching prediction)

2 x AZP

0.95

0.87 ± 0.05

2 x (5S,8S,14R)-ETHYL 11-(3-AMINO-3-OXOPROPYL)-8-BENZYL-14-HYDROXY-5-ISOBUTYL-3,6,9,12-TETRAOXO-1-PHENYL-2-OXA-4,7,10,11-TETRAAZAPENTADECAN-15-OATE

AZP.1:

23 residues within 4Å:

Chain A: T.25, T.26, H.41, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, P.168, H.172, D.187, R.188, Q.189, T.190, A.191, Q.192

15 PLIP interactions:

AZP.4:

23 residues within 4Å:

Chain B: T.25, T.26, H.41, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, P.168, H.172, D.187, R.188, Q.189, T.190, A.191, Q.192

16 PLIP interactions:

QMEANDisCo Local

QMEAN Z-Scores

Template	Seq Identity	Coverage	Description
2a5i.1.A	96.08%		3C-like peptidase Crystal structures of SARS coronavirus main peptidase inhibited by an aza-peptide epoxide in the space group C2

Model-Template Alignment

Biounit Oligo State	Homo-dimer
QSQE	0.95
Method	X-ray, 1.48 Å
Seq Similarity	0.63
Coverage	1.00
Range	1-304

Biounit Oligo State	Homo-dimer
QSQE	0.97
Method	X-ray, 1.59 Å
Seq Similarity	0.63
Coverage	1.00
Range	1-304

Biounit Oligo State	Homo-dimer
QSQE	0.99
Method	X-ray, 2.16 Å
Seq Similarity	0.63
Coverage	1.00
Range	1-306

Biounit Oligo State	Homo-dimer
QSQE	0.95
Method	X-ray, 1.95 Å
Seq Similarity	0.62
Coverage	1.00
Range	1-302

Biounit Oligo State	Homo-dimer
QSQE	1.00
Method	X-ray, 2.20 Å
Seq Similarity	0.63
Coverage	1.00
Range	1-301

3C-like proteinase nsp5 (3CL-PRO) | P0DTD1 PRO_0000449623

Created: May 18, 2022 at 17:42

Model Results

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Click model image to view in 3D

Ligand	Added to Model	Description
AZP	✓	(5S,8S,14R)-ETHYL 11-(3-AMINO…
AZP	✓	(5S,8S,14R)-ETHYL 11-(3-AMINO…
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
GOL	✕ - Not biologically relevant.	GLYCEROL
GOL	✕ - Not biologically relevant.	GLYCEROL

3C-like proteinase nsp5 (3CL-PRO) | P0DTD1 PRO_0000449623

Created: May 18, 2022 at 17:42

Model Results

Background

Resolution

Click model image to view in 3D

Click model image to view in 3D