scPDB - 3v0t entry

Protein Data Bank Entry:

PDB ID : 3v0t

Resolution :2.330 Å

Experimental Method : X-ray

Deposition Date : 2011-12-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Perakine reductase
ID:	PERR_RAUSE
AC:	Q3L181
Organism:	Rauvolfia serpentina
Reign:	Eukaryota
TaxID:	4060
EC Number:	1.1.1.317

Chains:

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

Ligand binding site composition:

B-Factor:	42.424
Number of residues:	24
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.831	617.625

% Hydrophobic	% Polar
47.54	52.46
According to VolSite

Ligand :

HET Code:	ATR
Formula:	C10H11N5O13P3
Molecular weight:	502.141 g/mol
DrugBank ID:	DB02363
Buried Surface Area:	55.29 %
Polar Surface area:	322.71 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
22.0383	12.5219	19.1339

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
O1B	OG	SER- 205	2.94	154.86	H-Bond (Protein Donor)	false
O2A	N	ILE- 207	3.2	156.16	H-Bond (Protein Donor)	false
O2A	N	GLY- 208	2.66	145.75	H-Bond (Protein Donor)	false
C4'	CD1	LEU- 211	4.36	0	Hydrophobic	false
C1'	CD1	LEU- 211	3.64	0	Hydrophobic	false
O1A	N	GLY- 279	2.64	168.21	H-Bond (Protein Donor)	false
O1P	OG1	THR- 280	3.42	131.39	H-Bond (Protein Donor)	false
O1P	N	THR- 281	2.89	155.23	H-Bond (Protein Donor)	false
O1P	OG1	THR- 281	2.76	173.25	H-Bond (Protein Donor)	false
O3P	NZ	LYS- 282	3.33	125.21	H-Bond (Protein Donor)	false
O3P	NZ	LYS- 282	3.33	0	Ionic (Protein Cationic)	false
O2P	ND2	ASN- 285	2.78	160.54	H-Bond (Protein Donor)	false
N6	O	ASN- 285	3.46	134.21	H-Bond (Ligand Donor)	false
N6	OD1	ASN- 288	3.39	137.52	H-Bond (Ligand Donor)	false
N7	ND2	ASN- 289	3.18	156.4	H-Bond (Protein Donor)	false
N6	OD1	ASN- 289	3	133.82	H-Bond (Ligand Donor)	false