scPDB - 3i0a entry

Protein Data Bank Entry:

PDB ID : 3i0a

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2009-06-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Neutrophil gelatinase-associated lipocalin
ID:	NGAL_HUMAN
AC:	P80188
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	75.971
Number of residues:	13
Including
Standard Amino Acids:	12
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	FE

Cavity properties

Ligandability	Volume (Å3)
0.889	519.750

% Hydrophobic	% Polar
60.39	39.61
According to VolSite

Ligand :

HET Code:	DBH
Formula:	C7H5O4
Molecular weight:	153.112 g/mol
DrugBank ID:	DB01672
Buried Surface Area:	48.32 %
Polar Surface area:	80.59 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
54.7727	103.727	39.4478

Binding mode :

What is Poseview ?

2D View
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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	OH	TYR- 106	3.1	166.3	H-Bond (Ligand Donor)	false
C9	CB	PHE- 123	4.08	0	Hydrophobic	false
C12	CG	LYS- 125	4.29	0	Hydrophobic	false
C6	CD	LYS- 125	3.72	0	Hydrophobic	false
O3	NZ	LYS- 125	3.29	138.93	H-Bond (Protein Donor)	false
C15	CB	TYR- 132	4.16	0	Hydrophobic	false
C12	CB	ALA- 134	3.72	0	Hydrophobic	false
O3	FE	FE- 179	2.33	0	Metal Acceptor	false
O6	FE	FE- 179	2.33	0	Metal Acceptor	false