scPDB - 3ocw entry

Protein Data Bank Entry:

PDB ID : 3ocw

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2010-08-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Lipoprotein E
ID:	HEL_HAEIN
AC:	P26093
Organism:	Haemophilus influenzae
Reign:	Bacteria
TaxID:	71421
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	14.584
Number of residues:	30
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.019	1464.750

% Hydrophobic	% Polar
46.54	53.46
According to VolSite

Ligand :

HET Code:	3AM
Formula:	C10H12N5O7P
Molecular weight:	345.205 g/mol
DrugBank ID:	-
Buried Surface Area:	58.1 %
Polar Surface area:	201.54 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
45.8146	-13.5599	-8.3563

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
O2P	N	ASN- 66	2.91	168.1	H-Bond (Protein Donor)	false
O3'	ND2	ASN- 66	2.7	138.89	H-Bond (Protein Donor)	false
C2'	CB	ASN- 66	3.96	0	Hydrophobic	false
DuAr	DuAr	PHE- 86	3.73	0	Aromatic Face/Face	false
C1'	CZ2	TRP- 91	3.92	0	Hydrophobic	false
O2P	OG1	THR- 124	2.73	168.2	H-Bond (Protein Donor)	false
O1P	N	ASN- 125	2.93	154.24	H-Bond (Protein Donor)	false
C5'	CB	ASN- 125	3.87	0	Hydrophobic	false
C4'	CB	ASN- 125	4.04	0	Hydrophobic	false
O1P	NZ	LYS- 161	3.02	146.72	H-Bond (Protein Donor)	false
O1P	NZ	LYS- 161	3.02	0	Ionic (Protein Cationic)	false
O2'	OH	TYR- 221	2.73	152.53	H-Bond (Ligand Donor)	false
C2'	CE1	TYR- 221	3.7	0	Hydrophobic	false
O3P	MG	MG- 263	2.28	0	Metal Acceptor	false
N6	O	HOH- 428	2.8	155.44	H-Bond (Ligand Donor)	false