scPDB - 1dgg entry

Protein Data Bank Entry:

PDB ID : 1dgg

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 1999-11-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Catalase
ID:	CATA_HUMAN
AC:	P04040
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.11.1.6

Chains:

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

Ligand binding site composition:

B-Factor:	44.747
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.920	678.375

% Hydrophobic	% Polar
59.20	40.80
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	54.81 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
13.7383	-8.01515	68.1915

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
C5N	CG	PRO- 151	3.85	0	Hydrophobic	false
O2D	NE2	HIS- 194	2.67	167.09	H-Bond (Ligand Donor)	false
C2D	CZ	PHE- 198	3.55	0	Hydrophobic	false
N6A	OG	SER- 201	3.06	157.3	H-Bond (Ligand Donor)	false
O2B	NH2	ARG- 203	3.22	159.56	H-Bond (Protein Donor)	false
O3X	NH1	ARG- 203	3.14	165.16	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 203	3.92	0	Ionic (Protein Cationic)	false
O1X	ND2	ASN- 213	2.59	135.01	H-Bond (Protein Donor)	false
O1X	NZ	LYS- 237	3.99	0	Ionic (Protein Cationic)	false
O2X	NZ	LYS- 237	3.54	0	Ionic (Protein Cationic)	false
C3N	CG1	VAL- 302	4.44	0	Hydrophobic	false
C3D	CG2	VAL- 302	3.76	0	Hydrophobic	false
N7N	O	TRP- 303	3.26	149.62	H-Bond (Ligand Donor)	false
O2N	N	HIS- 305	2.97	169.78	H-Bond (Protein Donor)	false
O3D	O	GLN- 442	3.07	130.95	H-Bond (Ligand Donor)	false
C2D	CB	PHE- 446	4.28	0	Hydrophobic	false
C5B	CG1	VAL- 450	4.27	0	Hydrophobic	false
C4D	CG2	VAL- 450	3.59	0	Hydrophobic	false
O7N	O	HOH- 4248	3.14	179.97	H-Bond (Protein Donor)	false