scPDB - 3v76 entry

Protein Data Bank Entry:

PDB ID : 3v76

Resolution :2.510 Å

Experimental Method : X-ray

Deposition Date : 2011-12-20

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:	Q92RY0_RHIME
AC:	Q92RY0
Organism:	Rhizobium meliloti
Reign:	Bacteria
TaxID:	266834
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	30.298
Number of residues:	68
Including
Standard Amino Acids:	60
Non Standard Amino Acids:	0
Water Molecules:	8
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.115	776.250

% Hydrophobic	% Polar
46.09	53.91
According to VolSite

Ligand :

HET Code:	FDA
Formula:	C27H33N9O15P2
Molecular weight:	785.550 g/mol
DrugBank ID:	-
Buried Surface Area:	66.02 %
Polar Surface area:	381.04 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	9
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
48.3991	-33.2794	2.11913

Binding mode :

What is Poseview ?

2D View
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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
O2A	N	ALA- 15	3.4	153.58	H-Bond (Protein Donor)	false
O1P	N	ALA- 16	2.76	155.55	H-Bond (Protein Donor)	false
O3B	OD1	ASP- 35	2.89	161.73	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 35	3.09	167.72	H-Bond (Ligand Donor)	false
N3A	N	HIS- 36	3.48	156.62	H-Bond (Protein Donor)	false
DuAr	DuAr	HIS- 36	3.49	0	Aromatic Face/Face	false
C8M	CD	LYS- 43	4.11	0	Hydrophobic	false
C7M	CD1	ILE- 46	3.78	0	Hydrophobic	false
C6	CB	SER- 47	3.84	0	Hydrophobic	false
C9A	CB	SER- 47	4.37	0	Hydrophobic	false
O4	N	GLY- 48	3.39	124.34	H-Bond (Protein Donor)	false
N3	O	ASN- 53	3.03	138.97	H-Bond (Ligand Donor)	false
O4	N	ASN- 53	3.48	132.31	H-Bond (Protein Donor)	false
C8M	CD1	ILE- 166	3.85	0	Hydrophobic	false
N7A	OG1	THR- 172	2.99	143.82	H-Bond (Protein Donor)	false
N6A	OG1	THR- 172	3.16	156.14	H-Bond (Ligand Donor)	false
C1'	CG	GLU- 339	3.98	0	Hydrophobic	false
C9	CG	GLU- 339	3.22	0	Hydrophobic	false
O3'	OE1	GLU- 368	3.18	130.33	H-Bond (Ligand Donor)	false
C5'	CB	GLU- 368	3.73	0	Hydrophobic	false
O2P	N	GLU- 368	2.92	174.88	H-Bond (Protein Donor)	false
C1'	CB	ASN- 402	4.43	0	Hydrophobic	false
C3'	CB	ASN- 402	4.45	0	Hydrophobic	false
O2	N	PHE- 403	2.59	149.8	H-Bond (Protein Donor)	false
C2'	CZ	PHE- 403	3.83	0	Hydrophobic	false
C4'	CE2	PHE- 403	3.84	0	Hydrophobic	false
O1A	O	HOH- 434	2.86	150.1	H-Bond (Protein Donor)	false
O4	O	HOH- 436	3.19	120.02	H-Bond (Protein Donor)	false
O2P	O	HOH- 440	2.9	179.98	H-Bond (Protein Donor)	false
N1	O	HOH- 499	2.57	179.95	H-Bond (Protein Donor)	false
O1P	O	HOH- 521	2.5	179.98	H-Bond (Protein Donor)	false