scPDB - 1bqo entry

Protein Data Bank Entry:

PDB ID : 1bqo

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 1998-08-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Stromelysin-1
ID:	MMP3_HUMAN
AC:	P08254
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.24.17

Chains:

Chain Name:	Percentage of Residues within binding site
B	100 %

Ligand binding site composition:

B-Factor:	17.627
Number of residues:	28
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.842	600.750

% Hydrophobic	% Polar
51.69	48.31
According to VolSite

Ligand :

HET Code:	N25
Formula:	C21H27N3O8S2
Molecular weight:	513.584 g/mol
DrugBank ID:	-
Buried Surface Area:	55.38 %
Polar Surface area:	159.3 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
1.29876	50.269	52.1732

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
C34	CE1	PHE- 86	3.76	0	Hydrophobic	false
C19	CG2	VAL- 163	4.25	0	Hydrophobic	false
C6	CB	LEU- 164	4.47	0	Hydrophobic	false
O12	N	LEU- 164	2.62	154.25	H-Bond (Protein Donor)	false
O12	N	ALA- 165	3.26	157.48	H-Bond (Protein Donor)	false
N25	O	ALA- 165	2.91	142.69	H-Bond (Ligand Donor)	false
C28	CB	HIS- 166	3.63	0	Hydrophobic	false
C5	CG1	VAL- 198	3.43	0	Hydrophobic	false
C8	CB	HIS- 201	3.82	0	Hydrophobic	false
C4	CB	HIS- 201	3.86	0	Hydrophobic	false
O26	OE2	GLU- 202	2.81	132.91	H-Bond (Ligand Donor)	false
O26	OE1	GLU- 202	3.31	167.21	H-Bond (Ligand Donor)	false
C8	CD1	LEU- 218	4.37	0	Hydrophobic	false
C17	CB	PRO- 221	4.23	0	Hydrophobic	false
C18	CB	PRO- 221	3.97	0	Hydrophobic	false
O24	ZN	ZN- 301	1.98	0	Metal Acceptor	false
O26	ZN	ZN- 301	1.87	0	Metal Acceptor	false