scPDB - 1xud entry

Protein Data Bank Entry:

PDB ID : 1xud

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2004-10-26

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
B	100 %

Ligand binding site composition:

B-Factor:	16.015
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)
1.210	786.375

% Hydrophobic	% Polar
46.78	53.22
According to VolSite

Ligand :

HET Code:	PB4
Formula:	C22H20F2N4O2
Molecular weight:	410.417 g/mol
DrugBank ID:	DB04760
Buried Surface Area:	72.89 %
Polar Surface area:	83.97 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
29.2373	-1.16383	61.0845

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
F1	CD1	LEU- 185	4.5	0	Hydrophobic	false
F2	CD2	PHE- 217	3.24	0	Hydrophobic	false
C2	CD2	LEU- 218	3.55	0	Hydrophobic	false
C17	CB	LEU- 218	4.34	0	Hydrophobic	false
C18	CD2	LEU- 218	4.46	0	Hydrophobic	false
C19	CG	LEU- 218	4.08	0	Hydrophobic	false
F1	CG1	VAL- 219	3.37	0	Hydrophobic	false
DuAr	DuAr	HIS- 222	3.7	0	Aromatic Face/Face	false
C21	CB	HIS- 222	3.34	0	Hydrophobic	false
N3	O	ALA- 238	3.28	122.34	H-Bond (Ligand Donor)	false
C19	CD1	LEU- 239	4.26	0	Hydrophobic	false
F1	CD1	TYR- 244	4.49	0	Hydrophobic	false
C4	CB	TYR- 244	4.2	0	Hydrophobic	false
O2	N	THR- 245	2.65	151.39	H-Bond (Protein Donor)	false
O1	N	THR- 247	2.75	177.61	H-Bond (Protein Donor)	false
C6	CB	PHE- 252	3.89	0	Hydrophobic	false
C15	CB	PHE- 252	3.65	0	Hydrophobic	false