scPDB - 4oay entry

Protein Data Bank Entry:

PDB ID : 4oay

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2014-01-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA-binding protein
ID:	F2RCL8_STRVP
AC:	F2RCL8
Organism:	Streptomyces venezuelae
Reign:	Bacteria
TaxID:	953739
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	41 %
M	11 %
N	48 %

Ligand binding site composition:

B-Factor:	39.290
Number of residues:	30
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	3
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.057	1049.625

% Hydrophobic	% Polar
24.76	75.24
According to VolSite

Ligand :

HET Code:	C2E
Formula:	C20H22N10O14P2
Molecular weight:	688.395 g/mol
DrugBank ID:	-
Buried Surface Area:	46.57 %
Polar Surface area:	366.32 Å2

Number of
H-Bond Acceptors:	20
H-Bond Donors:	6
Rings:	7
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
43.0247	-16.7829	19.2199

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
O3'	NZ	LYS- 84	3.48	133.73	H-Bond (Protein Donor)	false
O21	NZ	LYS- 84	2.81	150.2	H-Bond (Protein Donor)	false
C1A	CB	GLN- 113	4.23	0	Hydrophobic	false
N71	NE	ARG- 114	2.81	167.43	H-Bond (Protein Donor)	false
O61	NH2	ARG- 114	2.69	151.48	H-Bond (Protein Donor)	false
C4'	CB	SER- 123	4.25	0	Hydrophobic	false
C1'	CB	SER- 123	4	0	Hydrophobic	false
O1P	NH2	ARG- 125	2.82	171.92	H-Bond (Protein Donor)	false
N7	NE	ARG- 125	2.99	172.42	H-Bond (Protein Donor)	false
O6	NH2	ARG- 125	2.89	148.73	H-Bond (Protein Donor)	false
O2P	N	GLN- 126	2.99	160.66	H-Bond (Protein Donor)	false
N11	OD2	ASP- 128	2.7	164.13	H-Bond (Ligand Donor)	false
N21	OD1	ASP- 128	2.86	173.84	H-Bond (Ligand Donor)	false