scPDB - 3kry entry

Protein Data Bank Entry:

PDB ID : 3kry

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2009-11-19

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
D	100 %

Ligand binding site composition:

B-Factor:	20.302
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.916	486.000

% Hydrophobic	% Polar
40.28	59.72
According to VolSite

Ligand :

HET Code:	3KR
Formula:	C22H24F3N2O7S
Molecular weight:	517.495 g/mol
DrugBank ID:	-
Buried Surface Area:	60.75 %
Polar Surface area:	121.15 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	1
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
17.046	25.0817	9.28143

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
C19	CD2	LEU- 184	3.81	0	Hydrophobic	false
C21	CD2	LEU- 184	3.52	0	Hydrophobic	false
C23	CD2	LEU- 184	3.86	0	Hydrophobic	false
C7	CB	LEU- 185	4.33	0	Hydrophobic	false
C3	CD1	LEU- 185	4.25	0	Hydrophobic	false
O12	N	LEU- 185	2.6	155.23	H-Bond (Protein Donor)	false
N10	O	ALA- 186	3.19	135.48	H-Bond (Ligand Donor)	false
O12	N	ALA- 186	3.1	142.03	H-Bond (Protein Donor)	false
F33	CD1	LEU- 218	3.64	0	Hydrophobic	false
C29	CB	LEU- 218	3.92	0	Hydrophobic	false
C30	CG2	VAL- 219	4.3	0	Hydrophobic	false
C6	CG1	VAL- 219	3.55	0	Hydrophobic	false
C5	CB	HIS- 222	4.1	0	Hydrophobic	false
C25	CB	HIS- 222	3.77	0	Hydrophobic	false
O11	OE2	GLU- 223	2.69	169.03	H-Bond (Protein Donor)	false
F34	CD1	LEU- 239	3.71	0	Hydrophobic	false
C15	CB	PRO- 242	3.93	0	Hydrophobic	false
C4	CB	TYR- 244	4.22	0	Hydrophobic	false
C30	CB	TYR- 244	4.39	0	Hydrophobic	false
O31	OG1	THR- 245	3.36	146.13	H-Bond (Protein Donor)	false
F35	CB	THR- 245	4.29	0	Hydrophobic	false
F33	CB	THR- 247	4.15	0	Hydrophobic	false
F35	CG2	THR- 247	3.44	0	Hydrophobic	false
O11	ZN	ZN- 4999	2.16	0	Metal Acceptor	false
O14	ZN	ZN- 4999	2.29	0	Metal Acceptor	false