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Secondary Structure
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Confidencegradient Confidenceclass Indels Chain Unique Chain Rainbow 2° Structure Clustal Hydrophobic Size Charged Polar Proline Ser/Thr Cysteine Aliphatic Aromatic No Colour
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NGL PV

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

### Created: May 5, 2023, 9:34 p.m. at 21:34

Order by:

Oligo-State
  Homo-dimer
  (matching prediction)
GMQE
  0.97
QMEANDisCo Global:
  0.91 ± 0.05

Ligands
  2 x T8J
  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
5rfv.1.B 3C-like proteinase
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102306

Seq Identity
  100.00%
Coverage

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

Ligand | Added to Model | Description
--- | --- | ---
T8J | ✓ | 1-[4-(thiophene-2-carbonyl)piperazin-1-yl]ethan-1-one
T8J | ✓ | 1-[4-(thiophene-2-carbonyl)piperazin-1-yl]ethan-1-one
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

Oligo-State
  Homo-dimer
  (matching prediction)
GMQE
  0.97
QMEANDisCo Global:
  0.91 ± 0.05

Ligands
  2 x HWH
  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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:M.165, A:Q.189 Hydrogen bonds: A:E.166, A:Q.189 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 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:M.165, B:Q.189 Hydrogen bonds: B:E.166, B:Q.189 pi-Stacking: B:H.41

QMEANDisCo Local
QMEAN Z-Scores

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

Seq Identity
  100.00%
Coverage

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

Ligand | Added to Model | Description
--- | --- | ---
HWH | ✓ | ~{N}-[2-(5-fluoranyl-1~{H}-indol-3-yl)ethyl]ethanamide
HWH | ✓ | ~{N}-[2-(5-fluoranyl-1~{H}-indol-3-yl)ethyl]ethanamide
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

Oligo-State
  Homo-dimer
  (matching prediction)
GMQE
  0.97
QMEANDisCo Global:
  0.89 ± 0.05

Ligands

QMEANDisCo Local
QMEAN Z-Scores

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

Seq Identity
  100.00%
Coverage

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

Ligand | Added to Model | Description
--- | --- | ---
02J-ALA-VAL-LEU-PJE-010 | ✕ - Clashing with protein. | N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE
02J-ALA-VAL-LEU-PJE-010 | ✕ - Clashing with protein. | N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE

Model-Template Alignment

Oligo-State
  Homo-dimer
  (matching prediction)
GMQE
  0.96
QMEANDisCo Global:
  0.89 ± 0.05

Ligands
  2 x DTZ
  2 x ZINC(II)HYDROGENSULFIDE

  DTZ.5: | 3 residues within 4Å: Chain B: H.41, C.145, H.164 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.41, B:C.145
  DTZ.6: | 5 residues within 4Å: Chain A: T.25, L.27, H.41, C.145, H.164 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.41, A:C.145

QMEANDisCo Local
QMEAN Z-Scores

Template
2z9j.1.A 3C-like proteinase
Complex structure of SARS-CoV 3C-like protease with EPDTC

Seq Identity
  96.08%
Coverage

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

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

Oligo-State
  Homo-dimer
  (matching prediction)
GMQE
  0.95
QMEANDisCo Global:
  0.88 ± 0.05

Ligands
  1 x GLY, 2 x O6K
  1 x GLYCINE

  GLY.1: | 3 residues within 4Å: Chain A: R.298, S.301, Chain B: S.123 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.301

  2 x ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate

  O6K.2: | 18 residues within 4Å: Chain A: T.26, H.41, M.49, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, L.167, H.172, D.187, Q.189, Chain B: S.1 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:N.142, A:M.165, A:D.187, A:Q.189 Hydrogen bonds: A:G.143, A:S.144, A:C.145, A:H.164, A:E.166, A:E.166, B:S.1
  O6K.3: | 18 residues within 4Å: Chain A: S.1, Chain B: T.26, H.41, M.49, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, L.167, P.168, D.187, R.188 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:N.142, B:M.165, B:E.166 Hydrogen bonds: B:G.143, B:S.144, B:S.144, B:C.145, B:H.164, B:E.166, B:E.166

QMEANDisCo Local
QMEAN Z-Scores

Template
6y2g.1.A 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)

Seq Identity
  100.00%
Coverage

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

Ligand | Added to Model | Description
--- | --- | ---
GLY | ✓ | GLYCINE
O6K | ✓ | ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate
O6K | ✓ | ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate

Model-Template Alignment

Oligo-State
  Homo-dimer
  (matching prediction)
GMQE
  0.95
QMEANDisCo Global:
  0.87 ± 0.05

Ligands
  2 x AZP
  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: 15 interactions with chain A Hydrophobic interactions: A:H.41, A:M.49, A:P.168, A:Q.189 Hydrogen bonds: A:F.140, A:N.142, A:G.143, A:S.144, A:S.144, A:C.145, A:H.164, A:E.166, A:E.166, A:Q.189 Salt bridges: A:H.41
  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: 16 interactions with chain B Hydrophobic interactions: B:H.41, B:M.49, B:P.168, B:Q.189 Hydrogen bonds: B:F.140, B:N.142, B:G.143, B:S.144, B:S.144, B:C.145, B:H.164, B:E.166, B:E.166, B:E.166, B:Q.189 Salt bridges: B:H.41

QMEANDisCo Local
QMEAN Z-Scores

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

Seq Identity
  96.08%
Coverage

Biounit Oligo State | Homo-dimer
QSQE | 0.92
Method | X-ray, 1.88 Å
Seq Similarity | 0.62
Coverage | 1.00
Range | 1-306

Ligand | Added to Model | Description
--- | --- | ---
AZP | ✓ | (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 | ✓ | (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
EDO | ✕ - Not biologically relevant. | 1,2-ETHANEDIOL
EDO | ✕ - Not biologically relevant. | 1,2-ETHANEDIOL
GOL | ✕ - Not biologically relevant. | GLYCEROL
GOL | ✕ - Not biologically relevant. | GLYCEROL

Model-Template Alignment

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