scPDB - 4gnc entry

Protein Data Bank Entry:

PDB ID : 4gnc

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2012-08-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Regucalcin
ID:	RGN_HUMAN
AC:	Q15493
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.1.1.17

Chains:

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

Ligand binding site composition:

B-Factor:	21.813
Number of residues:	25
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
0.645	725.625

% Hydrophobic	% Polar
54.42	45.58
According to VolSite

Ligand :

HET Code:	ASO
Formula:	C6H12O5
Molecular weight:	164.156 g/mol
DrugBank ID:	-
Buried Surface Area:	64.78 %
Polar Surface area:	90.15 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	1
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
7.74109	2.98709	30.59

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
C5	SG	CYS- 16	4.29	0	Hydrophobic	false
C3	SG	CYS- 16	4.02	0	Hydrophobic	false
C3	CG	GLU- 18	4.02	0	Hydrophobic	false
C3	CD1	ILE- 34	4.21	0	Hydrophobic	false
O3	OD1	ASN- 103	2.83	160.61	H-Bond (Ligand Donor)	false
O4	OD1	ASN- 103	2.58	151.99	H-Bond (Ligand Donor)	false
O3	ND2	ASN- 103	3.2	120.59	H-Bond (Protein Donor)	false
C6	CE	MET- 118	4.17	0	Hydrophobic	false
O2	OD2	ASP- 204	2.6	162.82	H-Bond (Ligand Donor)	false
C1	CD1	TYR- 219	4.17	0	Hydrophobic	false
C1	CG2	THR- 246	4.09	0	Hydrophobic	false
O2	CA	CA- 301	2.41	0	Metal Acceptor	false
O3	CA	CA- 301	2.47	0	Metal Acceptor	false