university lille north of france LigASite database of binding sites
holo-structureHelp

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

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3iwm
HYDROLASE HEADER
THE OCTAMERIC SARS-COV MAIN PROTEASE TITLE
3C-LIKE PROTEINASE COMPND
Illustration of Binding SiteHelp

Figure showing the binding site residues. Ligands are displayed as CPK. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR). Ligands do not appear on the picture when PISA fails to apply symmetry operations to ligand coordinates.

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HETgroup - Residue ContactsHelp

List of binding site residues detected in this holo-structure.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the number of holo-structures where the residue is in contact with a ligand.
Column 2 gives the identifier of the chain to which the residue belongs.
Column 3 gives the 3-letter amino acid code, coloured according to physico-chemical type.

The binding residues in this holo structure are listed for each ligand independently, following the ligand's unique ID.

Note that since PISA files are used whenever available, chain identifiers may differ from those in original PDB files.

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3IH J1001
1E SER
24I THR
25I THR
26I THR
27I LEU
41I HIS
42I VAL
44I CYS
46I ALA
49I MET
52I PRO
54I TYR
140I PHE
141I LEU
142I ASN
143I GLY
144I SER
145I CYS
163I HIS
164I HIS
165I MET
166I GLU
167I LEU
168I PRO
187I ASP
188I ARG
189I GLN
190I THR
191I ALA
192I GLN
3IH F1001
1I SER
24E THR
25E THR
26E THR
27E LEU
41E HIS
44E CYS
45E THR
46E ALA
49E MET
54E TYR
140E PHE
141E LEU
142E ASN
143E GLY
144E SER
145E CYS
163E HIS
164E HIS
165E MET
166E GLU
167E LEU
168E PRO
172E HIS
187E ASP
188E ARG
189E GLN
190E THR
192E GLN
3IH H1001
1C SER
24G THR
25G THR
26G THR
27G LEU
41G HIS
50G LEU
54G TYR
119G ASN
140G PHE
141G LEU
142G ASN
143G GLY
144G SER
145G CYS
163G HIS
164G HIS
165G MET
166G GLU
167G LEU
168G PRO
172G HIS
187G ASP
188G ARG
189G GLN
190G THR
191G ALA
192G GLN
3IH N1001
1A SER
24M THR
25M THR
26M THR
27M LEU
41M HIS
44M CYS
45M THR
46M ALA
49M MET
54M TYR
140M PHE
141M LEU
142M ASN
143M GLY
144M SER
145M CYS
163M HIS
164M HIS
165M MET
166M GLU
167M LEU
168M PRO
172M HIS
187M ASP
188M ARG
189M GLN
190M THR
192M GLN
3IH L1001
1O SER
24K THR
25K THR
26K THR
27K LEU
41K HIS
44K CYS
45K THR
46K ALA
49K MET
54K TYR
140K PHE
141K LEU
142K ASN
143K GLY
144K SER
145K CYS
163K HIS
164K HIS
165K MET
166K GLU
167K LEU
168K PRO
172K HIS
187K ASP
188K ARG
189K GLN
190K THR
191K ALA
192K GLN
3IH P1001
1K SER
24O THR
25O THR
26O THR
27O LEU
41O HIS
50O LEU
54O TYR
119O ASN
140O PHE
141O LEU
142O ASN
143O GLY
144O SER
145O CYS
163O HIS
164O HIS
165O MET
166O GLU
167O LEU
168O PRO
172O HIS
187O ASP
188O ARG
189O GLN
190O THR
191O ALA
192O GLN
3IH D1001
1G SER
24C THR
25C THR
26C THR
27C LEU
41C HIS
42C VAL
44C CYS
45C THR
46C ALA
49C MET
54C TYR
140C PHE
141C LEU
142C ASN
143C GLY
144C SER
145C CYS
163C HIS
164C HIS
165C MET
166C GLU
167C LEU
168C PRO
172C HIS
187C ASP
188C ARG
189C GLN
190C THR
191C ALA
192C GLN
3IH B1001
1M SER
24A THR
25A THR
26A THR
27A LEU
41A HIS
42A VAL
44A CYS
46A ALA
49A MET
52A PRO
54A TYR
140A PHE
141A LEU
142A ASN
143A GLY
144A SER
145A CYS
163A HIS
164A HIS
165A MET
166A GLU
167A LEU
168A PRO
172A HIS
187A ASP
188A ARG
189A GLN
190A THR
191A ALA
192A GLN
External LinksHelp

PDB The Protein Data Bank
CSA Catalytic Site Atlas
PDBSum Overview of the macromolecular structure
CATH Protein Structure Classification
Scop Structural Classification of Proteins
Pfam Protein Families and Domains
UniProt Universal Protein Resource

LIGPLOT (only on holo-pages) is hosted at the EBI.

The LigPlot Jmol links point directly to the Jmol visualisation interface provided on the PDBSum page.

Note that due to different software used, the atomic contacts of LigPlot and LigASite do not necessarily correspond.

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Links to external databases:

LigPlot (hosted at the EBI):

Download FilesHelp

Several files are provided for download:

• The XML file defining the residue-ligand contacts; this file contains data on the apo and all holo-structures.
• The XML Schema file defining the semantics of the XML file
• 3D coordinates of the structure used in constructing LigASite (PISA structure file whenever available, PDB file otherwise.
• 3D coordinates of the combined binding residues in the apo structure
• 3D coordinates of the binding residues of the holo structure (only on the holo page)

Coordinate files are in PDB format.

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Hide table of related structures
Help

List of related structure, containing both the apo-structure and other holo-structures.

Column 1 gives the PDB ID and column 2 the unique ID of the ligands (holo-structures only).

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apo-structure
pdb ID
2c3s Details
other holo-structures
pdb ID Ligand Unique ID
2zu4 ZU3B_501 Details
ZU3A_501
2gz7 D3FB_307 Details
D3FD_307
3sn8 S89D_307 Details
S89B_307
2hob 3IHA1145 Details
2a5i AZPD_307 Details
AZPB_307
2gz8 F3FB_307 Details
F3FD_307
2gx4 NOLD2001 Details
NOLB2001
2z3c 0E2A_503 Details
0E2C_503
2zu5 ZU5B2001 Details
ZU5A2001
Ligand ListHelp

Ligands present in this holo structure.

Column 1 shows the ligand HET code
Column 2 shows the name, chemical formula and (non-stereo) SMILES string.

Data in column 2 appears as 'not_found' when it is not present in the file 'pdb2smiles.xml' from www.rcsb.org.

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3IH NAME: 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
FORMULA: C35 H48 N6 O8
SMILES: CC(C)CC(NC(=O)C(NC(=O)C(C)NC(=O)c1cc(C)on1)C(C)C)C(=O)NC(CC2CCNC2=O)C=CC(=O)OCc3ccccc3
v9.7
April 2012
Interdisciplinary Research Institute, Computational Biology, Villeneuve d'Ascq, France
University College London, Biomolecular Structure and Modelling Unit, London, UK
Hospital for Sick Children and University of Toronto, Structural Biology and Biochemistry Program, Toronto, Canada
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