scPDB - 1dgb entry

Protein Data Bank Entry:

PDB ID : 1dgb

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 1999-11-23

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:	64.430
Number of residues:	38
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.656	671.625

% Hydrophobic	% Polar
53.77	46.23
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	54.26 %
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
13.9601	-9.90971	66.7653

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
C5N	CG	PRO- 151	3.79	0	Hydrophobic	false
O2D	NE2	HIS- 194	3.02	174.96	H-Bond (Ligand Donor)	false
C2D	CZ	PHE- 198	3.76	0	Hydrophobic	false
N6A	OG	SER- 201	3.11	161.69	H-Bond (Ligand Donor)	false
O2B	NH2	ARG- 203	3.18	157.17	H-Bond (Protein Donor)	false
O3X	NH1	ARG- 203	2.76	171.45	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 203	3.7	0	Ionic (Protein Cationic)	false
O1X	ND2	ASN- 213	2.7	139.97	H-Bond (Protein Donor)	false
O1X	NZ	LYS- 237	3.56	0	Ionic (Protein Cationic)	false
O2X	NZ	LYS- 237	2.92	0	Ionic (Protein Cationic)	false
O2X	NZ	LYS- 237	2.92	160.2	H-Bond (Protein Donor)	false
C3N	CB	VAL- 302	4.07	0	Hydrophobic	false
C3D	CG2	VAL- 302	3.77	0	Hydrophobic	false
N7N	O	TRP- 303	3.2	145.22	H-Bond (Ligand Donor)	false
O2A	ND1	HIS- 305	3.08	156.71	H-Bond (Protein Donor)	false
O5B	ND1	HIS- 305	3.23	135.03	H-Bond (Protein Donor)	false
O1N	N	HIS- 305	2.93	157.3	H-Bond (Protein Donor)	false
O3D	O	GLN- 442	3.07	122.78	H-Bond (Ligand Donor)	false
C2D	CD1	PHE- 446	4.37	0	Hydrophobic	false
C5B	CG2	VAL- 450	4.45	0	Hydrophobic	false
C4D	CG2	VAL- 450	3.41	0	Hydrophobic	false
O7N	O	HOH- 1431	2.63	179.95	H-Bond (Protein Donor)	false