scPDB - 3dsz entry

Protein Data Bank Entry:

PDB ID : 3dsz

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2008-07-14

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:	20.003
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.990	837.000

% Hydrophobic	% Polar
44.76	55.24
According to VolSite

Ligand :

HET Code:	LIZ
Formula:	C30H41N5O13S
Molecular weight:	711.737 g/mol
DrugBank ID:	-
Buried Surface Area:	47.27 %
Polar Surface area:	328.41 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	6
Rings:	2
Aromatic rings:	1
Anionic atoms:	5
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	24

Mass center Coordinates

X	Y	Z
33.0583	78.2451	45.7682

Binding mode :

What is Poseview ?

2D View
3D View

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
O1	NE2	GLN- 33	3.3	170.88	H-Bond (Protein Donor)	false
O2	CZ	ARG- 36	3.52	0	Ionic (Protein Cationic)	false
C4	CG2	THR- 52	3.88	0	Hydrophobic	false
C25	CG2	THR- 52	4.48	0	Hydrophobic	false
O4	OG1	THR- 52	2.78	167.87	H-Bond (Protein Donor)	false
O8	NE2	GLN- 54	2.93	153.99	H-Bond (Protein Donor)	false
O4	NE2	GLN- 54	2.74	158.25	H-Bond (Protein Donor)	false
C17	CG1	VAL- 66	3.87	0	Hydrophobic	false
C12	CB	ALA- 68	3.72	0	Hydrophobic	false
C15	CB	ALA- 68	3.54	0	Hydrophobic	false
C25	CD	ARG- 70	4.2	0	Hydrophobic	false
C19	CD	ARG- 70	3.75	0	Hydrophobic	false
DuAr	CZ	ARG- 70	3.8	29.57	Pi/Cation	false
O12	OD1	ASP- 77	3.37	165.03	H-Bond (Ligand Donor)	false
C6	CD2	LEU- 79	3.85	0	Hydrophobic	false
C15	CD2	LEU- 79	3.89	0	Hydrophobic	false
C21	CD2	LEU- 79	4.1	0	Hydrophobic	false
C23	CB	LEU- 79	3.59	0	Hydrophobic	false
C14	SD	MET- 81	4.43	0	Hydrophobic	false
C17	SD	MET- 81	3.73	0	Hydrophobic	false
C18	CZ	PHE- 83	3.88	0	Hydrophobic	false
O10	OH	TYR- 106	2.51	153.03	H-Bond (Protein Donor)	false
C8	CZ	PHE- 123	3.77	0	Hydrophobic	false
C10	CE1	PHE- 123	3.5	0	Hydrophobic	false
O7	OG1	THR- 136	3.42	131.43	H-Bond (Protein Donor)	false
O8	OG1	THR- 136	2.73	154.37	H-Bond (Protein Donor)	false