scPDB - 4lmc entry

Protein Data Bank Entry:

PDB ID : 4lmc

Resolution :1.740 Å

Experimental Method : X-ray

Deposition Date : 2013-07-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Nucleoprotein
ID:	NCAP_CVHOC
AC:	P33469
Organism:	Human coronavirus OC43
Reign:	Viruses
TaxID:	31631
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.570
Number of residues:	25
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.790	388.125

% Hydrophobic	% Polar
56.52	43.48
According to VolSite

Ligand :

HET Code:	C5P
Formula:	C9H12N3O8P
Molecular weight:	321.181 g/mol
DrugBank ID:	DB03403
Buried Surface Area:	59.95 %
Polar Surface area:	190.61 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
19.7543	85.4724	-2.45224

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
N3	CZ	PHE- 57	2.59	168.52	Weak HBond LIG	false
N4	O	TYR- 62	3.21	131.28	H-Bond (Ligand Donor)	false
O2'	O	PHE- 66	2.87	129.15	H-Bond (Ligand Donor)	false
O3P	CZ	ARG- 122	3.28	0	Ionic (Protein Cationic)	false
O1P	CZ	ARG- 122	3.2	0	Ionic (Protein Cationic)	false
O2P	CZ	ARG- 122	3.24	0	Ionic (Protein Cationic)	false
C2'	CE1	TYR- 124	3.48	0	Hydrophobic	false
N4	OH	TYR- 126	3.04	129.25	H-Bond (Ligand Donor)	false
O2'	NH2	ARG- 164	3.13	136.09	H-Bond (Protein Donor)	false
C3'	CB	ALA- 171	3.46	0	Hydrophobic	false
O3P	O	HOH- 404	3	135.98	H-Bond (Protein Donor)	false