scPDB - 2ozr entry

Protein Data Bank Entry:

PDB ID : 2ozr

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2007-02-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Collagenase 3
ID:	MMP13_HUMAN
AC:	P45452
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.24

Chains:

Chain Name:	Percentage of Residues within binding site
H	100 %

Ligand binding site composition:

B-Factor:	23.110
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.564	580.500

% Hydrophobic	% Polar
41.28	58.72
According to VolSite

Ligand :

HET Code:	GG1
Formula:	C26H19N2O4
Molecular weight:	423.440 g/mol
DrugBank ID:	DB07827
Buried Surface Area:	66.91 %
Polar Surface area:	80.75 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	0
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
40.7391	-30.5061	27.6299

Binding mode :

What is Poseview ?

2D View
3D View

Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
O6	NZ	LYS- 119	2.91	145.31	H-Bond (Protein Donor)	false
O6	NZ	LYS- 119	2.91	0	Ionic (Protein Cationic)	false
O5	NZ	LYS- 119	3.51	0	Ionic (Protein Cationic)	false
C14	CG	LEU- 197	4.46	0	Hydrophobic	false
C17	CD1	LEU- 197	3.89	0	Hydrophobic	false
C22	CD1	LEU- 197	3.68	0	Hydrophobic	false
C9	CG2	VAL- 198	4.08	0	Hydrophobic	false
C9	CB	HIS- 201	3.7	0	Hydrophobic	false
C12	CB	HIS- 201	3.65	0	Hydrophobic	false
C14	CD1	LEU- 218	4.14	0	Hydrophobic	false
C7	CD1	LEU- 218	3.88	0	Hydrophobic	false
C18	CB	TYR- 223	3.83	0	Hydrophobic	false
C4	CB	THR- 226	4.37	0	Hydrophobic	false
C22	CG2	THR- 226	4.31	0	Hydrophobic	false
O2	N	THR- 226	3.28	135.55	H-Bond (Protein Donor)	false
C4	CG	LYS- 228	4.4	0	Hydrophobic	false
C25	CG	LYS- 228	4.46	0	Hydrophobic	false
C25	CD1	PHE- 231	3.74	0	Hydrophobic	false
C3	CE1	PHE- 231	3.4	0	Hydrophobic	false
C13	CB	PHE- 231	3.92	0	Hydrophobic	false
C25	CG	PRO- 234	4.36	0	Hydrophobic	false
C2	CG	PRO- 234	3.78	0	Hydrophobic	false