scPDB - 1g4k entry

Protein Data Bank Entry:

PDB ID : 1g4k

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2000-10-27

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
A	7 %
B	93 %

Ligand binding site composition:

B-Factor:	16.002
Number of residues:	29
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
1.276	1356.750

% Hydrophobic	% Polar
43.03	56.97
According to VolSite

Ligand :

HET Code:	HQQ
Formula:	C17H14N2O4
Molecular weight:	310.304 g/mol
DrugBank ID:	DB03368
Buried Surface Area:	74.53 %
Polar Surface area:	84.5 Å2

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

Mass center Coordinates

X	Y	Z
16.9807	49.6188	68.3238

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
O6	N	LEU- 164	2.77	171.42	H-Bond (Protein Donor)	false
C9	CD1	LEU- 164	4.3	0	Hydrophobic	false
N1	O	ALA- 165	2.68	174.96	H-Bond (Ligand Donor)	false
C15	CB	LEU- 197	4.15	0	Hydrophobic	false
C9	CG1	VAL- 198	4.43	0	Hydrophobic	false
C10	CG2	VAL- 198	3.95	0	Hydrophobic	false
C10	CB	HIS- 201	3.87	0	Hydrophobic	false
C18	CD1	LEU- 218	4.11	0	Hydrophobic	false
C12	CB	TYR- 223	3.87	0	Hydrophobic	false
N3	ZN	ZN- 301	2.12	0	Metal Acceptor	false