scPDB - 4ccq entry

Protein Data Bank Entry:

PDB ID : 4ccq

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2013-10-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thioredoxin reductase
ID:	C4LW95_ENTHI
AC:	C4LW95
Organism:	Entamoeba histolytica
Reign:	Eukaryota
TaxID:	5759
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	9 %
B	91 %

Ligand binding site composition:

B-Factor:	17.049
Number of residues:	37
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.804	1663.875

% Hydrophobic	% Polar
34.08	65.92
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	49.73 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-13.7845	20.7204	-26.1336

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
N7A	NZ	LYS- 122	3.23	165.51	H-Bond (Protein Donor)	false
O3B	N	GLY- 160	2.95	124.51	H-Bond (Protein Donor)	false
C2D	CB	ASP- 162	3.89	0	Hydrophobic	false
O2D	OD2	ASP- 162	2.65	168.1	H-Bond (Ligand Donor)	false
O1N	N	ALA- 163	3	160.91	H-Bond (Protein Donor)	false
O2B	NE	ARG- 183	3.29	128.93	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 183	3.47	126.53	H-Bond (Protein Donor)	false
O1X	NE	ARG- 183	2.68	160.18	H-Bond (Protein Donor)	false
O1X	NH2	ARG- 183	3.49	124.27	H-Bond (Protein Donor)	false
O2X	NH2	ARG- 183	3.09	170.56	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 183	3.5	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 183	3.9	164.07	Pi/Cation	false
C3B	CD	ARG- 188	3.95	0	Hydrophobic	false
O2X	NH2	ARG- 188	3.02	139.8	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 188	3.25	131.05	H-Bond (Protein Donor)	false
O3X	NE	ARG- 188	2.77	157.68	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 188	3.74	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 188	3.43	0	Ionic (Protein Cationic)	false
C1B	CG2	ILE- 246	4.18	0	Hydrophobic	false
O3D	O	TYR- 290	3.38	165.4	H-Bond (Ligand Donor)	false
O1A	NH2	ARG- 291	3.15	160.67	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 291	3.78	0	Ionic (Protein Cationic)	false
N3A	O	HOH- 2227	2.89	164.64	H-Bond (Protein Donor)	false
O1N	O	HOH- 2228	2.76	156.51	H-Bond (Protein Donor)	false