scPDB - 3kek entry

Protein Data Bank Entry:

PDB ID : 3kek

Resolution :1.970 Å

Experimental Method : X-ray

Deposition Date : 2009-10-26

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:	21.229
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.890	685.125

% Hydrophobic	% Polar
41.87	58.13
According to VolSite

Ligand :

HET Code:	3EK
Formula:	C24H25FN5O3
Molecular weight:	450.485 g/mol
DrugBank ID:	-
Buried Surface Area:	72.69 %
Polar Surface area:	112.83 Å2

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

Mass center Coordinates

X	Y	Z
46.1119	22.0329	17.7461

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
O31	NZ	LYS- 140	3.67	0	Ionic (Protein Cationic)	false
O33	NZ	LYS- 140	2.84	0	Ionic (Protein Cationic)	false
O33	NZ	LYS- 140	2.84	169.27	H-Bond (Protein Donor)	false
F32	CD1	LEU- 185	4.05	0	Hydrophobic	false
O31	ND2	ASN- 215	3.22	148.98	H-Bond (Protein Donor)	false
C5	CD2	PHE- 217	3.65	0	Hydrophobic	false
C18	CD2	LEU- 218	3.43	0	Hydrophobic	false
C13	CD1	LEU- 218	3.87	0	Hydrophobic	false
C29	CG	LEU- 218	4.31	0	Hydrophobic	false
F32	CG1	VAL- 219	3.42	0	Hydrophobic	false
C27	CG2	VAL- 219	4.35	0	Hydrophobic	false
DuAr	DuAr	HIS- 222	3.89	0	Aromatic Face/Face	false
C28	CB	HIS- 222	3.45	0	Hydrophobic	false
C28	CB	HIS- 222	3.45	0	Hydrophobic	false
N22	O	ALA- 238	3.22	135.17	H-Bond (Ligand Donor)	false
C19	CB	LEU- 239	3.86	0	Hydrophobic	false
C29	CD1	LEU- 239	4.25	0	Hydrophobic	false
F32	CD1	TYR- 244	4.32	0	Hydrophobic	false
C26	CB	TYR- 244	4.01	0	Hydrophobic	false
O21	N	THR- 245	2.75	166.9	H-Bond (Protein Donor)	false
C6	CE2	TYR- 246	3.85	0	Hydrophobic	false
N11	OG1	THR- 247	3.28	170.07	H-Bond (Protein Donor)	false
N11	N	THR- 247	2.93	162.87	H-Bond (Protein Donor)	false
C13	CG2	THR- 247	4.46	0	Hydrophobic	false
C1	CB	PHE- 252	4.17	0	Hydrophobic	false
C19	CE1	PHE- 252	3.79	0	Hydrophobic	false
C19	CG	PRO- 255	3.68	0	Hydrophobic	false
N9	O	HOH- 2049	3.21	179.99	H-Bond (Protein Donor)	false