scPDB - 3r5y entry

Protein Data Bank Entry:

PDB ID : 3r5y

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2011-03-20

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:	Q5YUF0_NOCFA
AC:	Q5YUF0
Organism:	Nocardia farcinica
Reign:	Bacteria
TaxID:	247156
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	26.111
Number of residues:	44
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.210	573.750

% Hydrophobic	% Polar
53.53	46.47
According to VolSite

Ligand :

HET Code:	F42
Formula:	C29H32N5O18P
Molecular weight:	769.561 g/mol
DrugBank ID:	DB03913
Buried Surface Area:	59.2 %
Polar Surface area:	389.68 Å2

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

Mass center Coordinates

X	Y	Z
4.05943	12.9859	-2.6283

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
C2I	CG	PRO- 13	4.39	0	Hydrophobic	false
C1'	CD1	ILE- 17	4.38	0	Hydrophobic	false
C9	CD1	ILE- 17	3.81	0	Hydrophobic	false
C7	CB	PHE- 35	4.06	0	Hydrophobic	false
C6	CD2	LEU- 40	3.56	0	Hydrophobic	false
C7	CD1	LEU- 40	3.92	0	Hydrophobic	false
C3G	CG	ARG- 48	4.33	0	Hydrophobic	false
O6G	NE	ARG- 48	2.74	165.96	H-Bond (Protein Donor)	false
O6G	CZ	ARG- 48	3.67	0	Ionic (Protein Cationic)	false
O2V	N	LYS- 49	2.73	143.53	H-Bond (Protein Donor)	false
C3G	CB	LYS- 49	4.24	0	Hydrophobic	false
O2V	OG1	THR- 50	3.34	142.16	H-Bond (Protein Donor)	false
O2V	N	THR- 50	2.79	154.22	H-Bond (Protein Donor)	false
O2W	OG1	THR- 50	2.76	158.04	H-Bond (Protein Donor)	false
C4H	CD	ARG- 54	4.12	0	Hydrophobic	false
O2W	NH1	ARG- 54	3.09	144.25	H-Bond (Protein Donor)	false
O2W	NE	ARG- 54	2.99	152.69	H-Bond (Protein Donor)	false
O2W	CZ	ARG- 54	3.47	0	Ionic (Protein Cationic)	false
C2'	CG2	THR- 56	3.46	0	Hydrophobic	false
O2'	O	PRO- 57	2.68	174.39	H-Bond (Ligand Donor)	false
C8	CB	PRO- 57	3.92	0	Hydrophobic	false
O4	N	MET- 59	3.12	175.29	H-Bond (Protein Donor)	false
C6	SD	MET- 59	4.09	0	Hydrophobic	false
N3	O	VAL- 70	2.92	157.92	H-Bond (Ligand Donor)	false
O2	N	SER- 72	3.16	120.9	H-Bond (Protein Donor)	false
O2	N	GLN- 73	2.8	157.96	H-Bond (Protein Donor)	false
C5'	CG	GLN- 73	3.95	0	Hydrophobic	false
C5'	CB	PRO- 80	3.67	0	Hydrophobic	false
O2P	N	ALA- 81	2.71	163.97	H-Bond (Protein Donor)	false
C4G	CB	ALA- 81	3.63	0	Hydrophobic	false
C4H	CB	ALA- 81	3.7	0	Hydrophobic	false
O4'	NE1	TRP- 82	2.99	153.13	H-Bond (Protein Donor)	false
O1P	N	TRP- 82	3.1	132.59	H-Bond (Protein Donor)	false
O5H	ND2	ASN- 85	2.94	154.8	H-Bond (Protein Donor)	false
O2U	O	HOH- 207	2.8	179.96	H-Bond (Protein Donor)	false