scPDB - 1gkc entry

Protein Data Bank Entry:

PDB ID : 1gkc

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2001-08-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Matrix metalloproteinase-9
ID:	MMP9_HUMAN
AC:	P14780
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.24.35

Chains:

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

Ligand binding site composition:

B-Factor:	27.104
Number of residues:	23
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.387	415.125

% Hydrophobic	% Polar
39.84	60.16
According to VolSite

Ligand :

HET Code:	NFH
Formula:	C15H29N3O4
Molecular weight:	315.408 g/mol
DrugBank ID:	-
Buried Surface Area:	59.37 %
Polar Surface area:	98.74 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	0
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
40.6682	14.3185	141.685

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
N2	O	GLY- 186	2.77	155.19	H-Bond (Ligand Donor)	false
O	N	LEU- 188	2.7	166.63	H-Bond (Protein Donor)	false
CG	CD1	LEU- 188	4.34	0	Hydrophobic	false
CD2	CG1	VAL- 398	4.07	0	Hydrophobic	false
CD2	CB	HIS- 401	4.23	0	Hydrophobic	false
OM	OE1	GLU- 402	2.65	165.79	H-Bond (Protein Donor)	false
N1	O	PRO- 421	3.49	166.41	H-Bond (Ligand Donor)	false
CG3	CG	MET- 422	3.75	0	Hydrophobic	false
O1	N	TYR- 423	2.82	165.79	H-Bond (Protein Donor)	false
CD2	CD1	TYR- 423	4.26	0	Hydrophobic	false
CG	CB	TYR- 423	4.17	0	Hydrophobic	false
OM	ZN	ZN- 1451	2.54	0	Metal Acceptor	false
ON	ZN	ZN- 1451	1.98	0	Metal Acceptor	false