scPDB - 1xur entry

Protein Data Bank Entry:

PDB ID : 1xur

Resolution :1.850 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
A	100 %

Ligand binding site composition:

B-Factor:	11.675
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.919	651.375

% Hydrophobic	% Polar
41.45	58.55
According to VolSite

Ligand :

HET Code:	PB5
Formula:	C18H16N6O2
Molecular weight:	348.359 g/mol
DrugBank ID:	DB04761
Buried Surface Area:	72.57 %
Polar Surface area:	109.76 Å2

Number of
H-Bond Acceptors:	6
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
-11.3967	26.674	46.9193

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
C2	CD2	LEU- 218	3.57	0	Hydrophobic	false
C24	CB	LEU- 218	4.46	0	Hydrophobic	false
C25	CD2	LEU- 218	4.44	0	Hydrophobic	false
C30	CG	LEU- 218	4.12	0	Hydrophobic	false
C31	CG2	VAL- 219	4.42	0	Hydrophobic	false
DuAr	DuAr	HIS- 222	3.8	0	Aromatic Face/Face	false
C31	CB	HIS- 222	3.39	0	Hydrophobic	false
N10	O	ALA- 238	3.25	120.56	H-Bond (Ligand Donor)	false
C30	CD1	LEU- 239	4.21	0	Hydrophobic	false
O42	N	THR- 245	2.66	151.63	H-Bond (Protein Donor)	false
C2	CG2	THR- 247	4.36	0	Hydrophobic	false
O41	OG1	THR- 247	3	165.95	H-Bond (Protein Donor)	false
O41	N	THR- 247	2.8	172.76	H-Bond (Protein Donor)	false
C18	CB	PHE- 252	4.17	0	Hydrophobic	false