scPDB - 2y4m entry

Protein Data Bank Entry:

PDB ID : 2y4m

Resolution :2.700 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:	39.409
Number of residues:	46
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	CL MG

Cavity properties

Ligandability	Volume (Å3)
1.008	1437.750

% Hydrophobic	% Polar
49.30	50.70
According to VolSite

Ligand :

HET Code:	GDX
Formula:	C16H20N5O17P2
Molecular weight:	616.301 g/mol
DrugBank ID:	DB04023
Buried Surface Area:	73.35 %
Polar Surface area:	372.61 Å2

Number of
H-Bond Acceptors:	20
H-Bond Donors:	7
Rings:	4
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
47.8516	-34.804	63.2068

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
C1D	CB	PRO- 7	4.38	0	Hydrophobic	false
O3D	O	PRO- 7	2.75	159.88	H-Bond (Ligand Donor)	false
O2D	N	LYS- 9	2.88	141.13	H-Bond (Protein Donor)	false
N2	O	ILE- 35	2.67	126.02	H-Bond (Ligand Donor)	false
N2	OE1	GLN- 66	3	125.44	H-Bond (Ligand Donor)	false
O3'	NZ	LYS- 76	3.09	147.3	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 100	2.59	159.63	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 100	2.9	126.62	H-Bond (Ligand Donor)	false
C4D	CB	ASP- 100	4.1	0	Hydrophobic	false
O3D	N	ALA- 101	2.91	141.22	H-Bond (Protein Donor)	false
O2'	O	LEU- 163	3.12	150.4	H-Bond (Ligand Donor)	false
O2'	N	GLY- 165	3.35	136.43	H-Bond (Protein Donor)	false
C5D	CZ3	TRP- 189	4.18	0	Hydrophobic	false
C5'	CZ3	TRP- 189	4.4	0	Hydrophobic	false
O4'	OD2	ASP- 192	2.56	169.99	H-Bond (Ligand Donor)	false
O2A	NH2	ARG- 218	3.48	149.15	H-Bond (Protein Donor)	false
C5'	SD	MET- 229	4.25	0	Hydrophobic	false
O1A	MG	MG- 400	2.12	0	Metal Acceptor	false
O3B	MG	MG- 400	1.95	0	Metal Acceptor	false