scPDB - 4g1c entry

Protein Data Bank Entry:

PDB ID : 4g1c

Resolution :1.940 Å

Experimental Method : X-ray

Deposition Date : 2012-07-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD-dependent protein deacylase sirtuin-5, mitochondrial
ID:	SIR5_HUMAN
AC:	Q9NXA8
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	98 %
B	2 %

Ligand binding site composition:

B-Factor:	33.697
Number of residues:	51
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.157	1107.000

% Hydrophobic	% Polar
47.87	52.13
According to VolSite

Ligand :

HET Code:	CNA
Formula:	C22H28N7O13P2
Molecular weight:	660.444 g/mol
DrugBank ID:	DB02498
Buried Surface Area:	73.9 %
Polar Surface area:	334.31 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
18.5855	5.60295	20.8205

Binding mode :

What is Poseview ?

2D View
3D View

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
O1A	N	ALA- 59	2.72	159.75	H-Bond (Protein Donor)	false
C5B	CB	ALA- 59	4.16	0	Hydrophobic	false
C2D	CB	ALA- 59	4.14	0	Hydrophobic	false
C4N	CB	ALA- 59	3.91	0	Hydrophobic	false
N6A	OE1	GLU- 64	3.04	150.64	H-Bond (Ligand Donor)	false
C4N	CG1	VAL- 67	4.33	0	Hydrophobic	false
C5B	CG2	THR- 69	4.19	0	Hydrophobic	false
O2N	N	PHE- 70	2.76	161.68	H-Bond (Protein Donor)	false
C4'	CE1	PHE- 70	3.43	0	Hydrophobic	false
C5N	CE2	PHE- 70	3.3	0	Hydrophobic	false
C5D	CD1	PHE- 70	3.72	0	Hydrophobic	false
C5B	CG	ARG- 71	3.96	0	Hydrophobic	false
C3B	CG	ARG- 71	4.01	0	Hydrophobic	false
O2A	NE2	GLN- 140	3.04	164.6	H-Bond (Protein Donor)	false
O2D	NE2	GLN- 140	3.39	163.47	H-Bond (Protein Donor)	false
C3D	CB	GLN- 140	4.36	0	Hydrophobic	false
O2D	OD1	ASN- 141	3.08	138.87	H-Bond (Ligand Donor)	false
O7N	N	ILE- 142	3.05	141.54	H-Bond (Protein Donor)	false
N7N	OD2	ASP- 143	2.79	164.38	H-Bond (Ligand Donor)	false
O3D	ND1	HIS- 158	3.48	120.12	H-Bond (Protein Donor)	false
C4D	CZ	PHE- 223	4.27	0	Hydrophobic	false
O2A	N	SER- 251	2.9	171.38	H-Bond (Protein Donor)	false
O2A	OG	SER- 251	2.72	174.21	H-Bond (Protein Donor)	false
C3B	CB	SER- 251	4.1	0	Hydrophobic	false
C3D	CG2	VAL- 254	4.1	0	Hydrophobic	false
O3B	ND2	ASN- 275	2.73	156.67	H-Bond (Protein Donor)	false
O2B	OD1	ASN- 275	2.93	158.64	H-Bond (Ligand Donor)	false
O2B	OG1	THR- 276	3.39	122.2	H-Bond (Protein Donor)	false
N1A	N	CYS- 293	2.84	155.44	H-Bond (Protein Donor)	false