scPDB - 4xnw entry

Protein Data Bank Entry:

PDB ID : 4xnw

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2015-01-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	9.110	9.110	9.110	0.000	9.110	2

List of CHEMBLId :

CHEMBL444278

Binding Site :

Uniprot Annotation

Name:	P2Y purinoceptor 1
ID:	P2RY1_HUMAN
AC:	P47900
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	0.000
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.313	607.500

% Hydrophobic	% Polar
35.00	65.00
According to VolSite

Ligand :

HET Code:	2ID
Formula:	C13H14IN5O8P2
Molecular weight:	557.131 g/mol
DrugBank ID:	-
Buried Surface Area:	62.67 %
Polar Surface area:	220.09 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	1
Rings:	4
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
20.026	22.7726	9.74203

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
I2	CB	CYS- 42	3.7	0	Hydrophobic	false
I2	CD1	LEU- 44	4.14	0	Hydrophobic	false
CAA	CD1	LEU- 44	4.49	0	Hydrophobic	false
CAK	CD2	LEU- 44	3.61	0	Hydrophobic	false
OAF	NZ	LYS- 46	2.92	159.13	H-Bond (Protein Donor)	false
OAF	NZ	LYS- 46	2.92	0	Ionic (Protein Cationic)	false
OAG	NZ	LYS- 46	3.41	0	Ionic (Protein Cationic)	false
OAC	NZ	LYS- 46	3.66	0	Ionic (Protein Cationic)	false
OAF	CZ	ARG- 195	3.52	0	Ionic (Protein Cationic)	false
OAC	CZ	ARG- 195	3.88	0	Ionic (Protein Cationic)	false
OAF	NH2	ARG- 195	3.11	140.56	H-Bond (Protein Donor)	false
OAF	NE	ARG- 195	3.07	145.99	H-Bond (Protein Donor)	false
OAC	NH2	ARG- 195	2.72	142.97	H-Bond (Protein Donor)	false
OAC	OG1	THR- 201	3.47	172.1	H-Bond (Protein Donor)	false
CAJ	CD1	TYR- 203	4.2	0	Hydrophobic	false
CAL	CE1	TYR- 203	3.69	0	Hydrophobic	false
OAD	N	ASP- 204	3	131.97	H-Bond (Protein Donor)	false
OAD	OG1	THR- 205	2.82	175.41	H-Bond (Protein Donor)	false
OAD	N	THR- 205	2.85	152.21	H-Bond (Protein Donor)	false
N7	ND2	ASN- 283	3.11	154.8	H-Bond (Protein Donor)	false
N6	OD1	ASN- 283	2.62	135.26	H-Bond (Ligand Donor)	false
CAA	CB	ALA- 286	3.59	0	Hydrophobic	false
CAA	CB	ASN- 299	3.91	0	Hydrophobic	false
CAK	CE1	TYR- 303	4.5	0	Hydrophobic	false
CAA	CB	TYR- 303	3.92	0	Hydrophobic	false
OAE	OH	TYR- 306	3.39	142.44	H-Bond (Protein Donor)	false
OAB	NH1	ARG- 310	2.52	167.5	H-Bond (Protein Donor)	false
OAB	NH2	ARG- 310	3.42	123.08	H-Bond (Protein Donor)	false
OAB	CZ	ARG- 310	3.39	0	Ionic (Protein Cationic)	false