scPDB - 3kec entry

Protein Data Bank Entry:

PDB ID : 3kec

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2009-10-25

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
A	100 %

Ligand binding site composition:

B-Factor:	21.823
Number of residues:	37
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.966	475.875

% Hydrophobic	% Polar
48.94	51.06
According to VolSite

Ligand :

HET Code:	3KE
Formula:	C24H20N5O4
Molecular weight:	442.447 g/mol
DrugBank ID:	-
Buried Surface Area:	71.75 %
Polar Surface area:	122.06 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	4
Aromatic rings:	4
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
84.1432	12.4135	34.3293

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
O5	NZ	LYS- 140	3.34	129.42	H-Bond (Protein Donor)	false
O5	NZ	LYS- 140	3.34	0	Ionic (Protein Cationic)	false
C13	CD1	LEU- 185	4.32	0	Hydrophobic	false
O4	ND2	ASN- 215	3.08	144	H-Bond (Protein Donor)	false
C19	CG	LEU- 218	4.37	0	Hydrophobic	false
C23	CD1	LEU- 218	3.64	0	Hydrophobic	false
C13	CG1	VAL- 219	3.95	0	Hydrophobic	false
C17	CG2	VAL- 219	4.43	0	Hydrophobic	false
C13	CB	HIS- 222	4.42	0	Hydrophobic	false
C17	CB	HIS- 222	3.47	0	Hydrophobic	false
DuAr	DuAr	HIS- 222	4	0	Aromatic Face/Face	false
C19	CD1	LEU- 239	4.14	0	Hydrophobic	false
C15	CB	TYR- 244	4.31	0	Hydrophobic	false
N3	N	THR- 245	2.86	165.48	H-Bond (Protein Donor)	false
O3	N	THR- 247	3.19	160.95	H-Bond (Protein Donor)	false
C8	CG2	THR- 247	3.76	0	Hydrophobic	false
C14	CB	PHE- 252	3.85	0	Hydrophobic	false
C2	CG	PRO- 255	4.11	0	Hydrophobic	false
N2	O	HOH- 319	3.24	138.23	H-Bond (Ligand Donor)	false