scPDB - 2yig entry

Protein Data Bank Entry:

PDB ID : 2yig

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2011-05-13

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
B	100 %

Ligand binding site composition:

B-Factor:	15.172
Number of residues:	32
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.961	604.125

% Hydrophobic	% Polar
45.25	54.75
According to VolSite

Ligand :

HET Code:	5EL
Formula:	C28H28N3O3
Molecular weight:	454.540 g/mol
DrugBank ID:	-
Buried Surface Area:	55.73 %
Polar Surface area:	75.89 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	6
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
53.3288	-14.3495	24.1694

Binding mode :

What is Poseview ?

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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
C28	CD2	LEU- 184	3.59	0	Hydrophobic	false
C25	CD1	LEU- 184	3.8	0	Hydrophobic	false
C19	CG	LEU- 185	4.19	0	Hydrophobic	false
C20	CB	LEU- 185	4.18	0	Hydrophobic	false
C18	CD1	LEU- 185	4.15	0	Hydrophobic	false
O3	N	LEU- 185	3.01	172.2	H-Bond (Protein Donor)	false
C5	CB	LEU- 218	3.96	0	Hydrophobic	false
C4	CG2	VAL- 219	4.15	0	Hydrophobic	false
C21	CG1	VAL- 219	4.03	0	Hydrophobic	false
C3	CB	HIS- 222	3.63	0	Hydrophobic	false
C16	CB	HIS- 222	4.28	0	Hydrophobic	false
C14	CD1	LEU- 239	4.46	0	Hydrophobic	false
C6	CD1	LEU- 239	4.09	0	Hydrophobic	false
N2	O	PRO- 242	3.48	166.16	H-Bond (Ligand Donor)	false
C17	CB	TYR- 244	3.99	0	Hydrophobic	false
O1	OG1	THR- 245	3.3	157.6	H-Bond (Protein Donor)	false
C14	CE1	PHE- 252	3.7	0	Hydrophobic	false
C12	CG	PRO- 255	3.97	0	Hydrophobic	false