scPDB - 2y4l entry

Protein Data Bank Entry:

PDB ID : 2y4l

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2011-01-07

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:	D0MI02_RHOM4
AC:	D0MI02
Organism:	Rhodothermus marinus
Reign:	Bacteria
TaxID:	518766
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	50.221
Number of residues:	37
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.786	1198.125

% Hydrophobic	% Polar
47.61	52.39
According to VolSite

Ligand :

HET Code:	GDP
Formula:	C10H12N5O11P2
Molecular weight:	440.177 g/mol
DrugBank ID:	DB04315
Buried Surface Area:	68.61 %
Polar Surface area:	276.39 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
97.0968	-24.8035	114.47

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
O3'	O	PRO- 7	2.67	146.91	H-Bond (Ligand Donor)	false
O2'	N	LYS- 9	3.17	134.86	H-Bond (Protein Donor)	false
N2	O	ILE- 35	3.12	133.22	H-Bond (Ligand Donor)	false
N1	OE1	GLN- 66	2.53	161.65	H-Bond (Ligand Donor)	false
N2	OE1	GLN- 66	3.05	130.22	H-Bond (Ligand Donor)	false
C1'	CG	LYS- 76	4.41	0	Hydrophobic	false
C4'	CB	ASP- 100	4	0	Hydrophobic	false
O3'	N	ALA- 101	2.73	176.14	H-Bond (Protein Donor)	false
C5'	CH2	TRP- 189	4.2	0	Hydrophobic	false
O3B	NZ	LYS- 215	4	0	Ionic (Protein Cationic)	false
O1A	NH2	ARG- 218	3.17	150.26	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 218	3.96	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 218	3.85	0	Ionic (Protein Cationic)	false
O3B	MN	MN- 400	2.17	0	Metal Acceptor	false
O2A	MN	MN- 400	2.33	0	Metal Acceptor	false
N7	O	HOH- 2005	3.44	150.91	H-Bond (Protein Donor)	false