scPDB - 4j4b entry

Protein Data Bank Entry:

PDB ID : 4j4b

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2013-02-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein
ID:	Q46E80_METBF
AC:	Q46E80
Organism:	Methanosarcina barkeri
Reign:	Archaea
TaxID:	269797
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	90 %
B	10 %

Ligand binding site composition:

B-Factor:	40.635
Number of residues:	52
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	3
Water Molecules:	2
Cofactors:
Metals:	NA MG

Cavity properties

Ligandability	Volume (Å3)
0.323	2389.500

% Hydrophobic	% Polar
45.76	54.24
According to VolSite

Ligand :

HET Code:	NAI
Formula:	C21H27N7O14P2
Molecular weight:	663.425 g/mol
DrugBank ID:	DB00157
Buried Surface Area:	63.72 %
Polar Surface area:	342.9 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	6
Rings:	5
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-11.2856	26.6048	-21.4947

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
O2D	O	ALA- 2	2.9	163.21	H-Bond (Ligand Donor)	false
C3D	CB	ALA- 2	4.09	0	Hydrophobic	false
C4N	CG2	THR- 125	3.68	0	Hydrophobic	false
O2A	NZ	LYS- 151	3.55	0	Ionic (Protein Cationic)	false
O2A	N	LYS- 151	3.06	177	H-Bond (Protein Donor)	false
O2N	N	VAL- 152	2.98	151.07	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 152	4.27	0	Hydrophobic	false
O3B	OD1	ASP- 171	3.49	130.1	H-Bond (Ligand Donor)	false
O3B	OD2	ASP- 171	2.79	172.95	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 171	2.61	156.42	H-Bond (Ligand Donor)	false
N3A	N	ALA- 172	3.19	152.6	H-Bond (Protein Donor)	false
C3B	CD1	LEU- 176	4.41	0	Hydrophobic	false
O4B	OG1	THR- 204	3.13	161.62	H-Bond (Protein Donor)	false
C3D	CB	PRO- 205	4.06	0	Hydrophobic	false
N7N	O	PRO- 224	2.84	151.14	H-Bond (Ligand Donor)	false
N7N	O	GLU- 245	2.85	173.53	H-Bond (Ligand Donor)	false
O7N	MG	MG- 903	2.19	0	Metal Acceptor	false
C4N	C16	0TF- 904	3.41	0	Hydrophobic	false
O7N	O	HOH- 1003	2.92	179.97	H-Bond (Protein Donor)	false
O2N	O	HOH- 1005	2.63	173.06	H-Bond (Protein Donor)	false