scPDB - 2d1n entry

Protein Data Bank Entry:

PDB ID : 2d1n

Resolution :2.370 Å

Experimental Method : X-ray

Deposition Date : 2005-08-29

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:	54.715
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)
0.622	459.000

% Hydrophobic	% Polar
33.82	66.18
According to VolSite

Ligand :

HET Code:	FA4
Formula:	C24H44N6O3
Molecular weight:	464.645 g/mol
DrugBank ID:	-
Buried Surface Area:	58.69 %
Polar Surface area:	169.7 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	7
Rings:	1
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	19

Mass center Coordinates

X	Y	Z
-43.4237	26.7482	-17.3001

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
C23	CZ	TYR- 176	3.91	0	Hydrophobic	false
C20	CD2	LEU- 184	3.81	0	Hydrophobic	false
C14	CD1	LEU- 185	4.25	0	Hydrophobic	false
O19	N	LEU- 185	2.85	164.85	H-Bond (Protein Donor)	false
O19	N	ALA- 186	3.31	171.27	H-Bond (Protein Donor)	false
C1	CD2	LEU- 218	3.8	0	Hydrophobic	false
C2	CB	LEU- 218	3.99	0	Hydrophobic	false
C8	CB	HIS- 222	3.82	0	Hydrophobic	false
N31	O	PRO- 236	2.73	140.69	H-Bond (Ligand Donor)	false
N28	O	ALA- 238	2.89	128.28	H-Bond (Ligand Donor)	false
C8	CD1	LEU- 239	4.42	0	Hydrophobic	false
C6	CD1	LEU- 239	4.03	0	Hydrophobic	false
C27	CB	PHE- 241	4.14	0	Hydrophobic	false
C10	CB	TYR- 244	4.28	0	Hydrophobic	false
C9	CD1	TYR- 244	4.05	0	Hydrophobic	false
O32	ZN	ZN- 270	1.94	0	Metal Acceptor	false
O33	ZN	ZN- 270	2.34	0	Metal Acceptor	false