scPDB - 2ome entry

Protein Data Bank Entry:

PDB ID : 2ome

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2007-01-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	C-terminal-binding protein 2
ID:	CTBP2_HUMAN
AC:	P56545
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	48.970
Number of residues:	47
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.596	840.375

% Hydrophobic	% Polar
35.34	64.66
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	69.29 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
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
9.25461	-2.87636	7.99089

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
C4N	CG2	THR- 134	3.84	0	Hydrophobic	false
O2A	NH1	ARG- 190	3.11	121.12	H-Bond (Protein Donor)	false
O2A	N	ARG- 190	2.85	168.6	H-Bond (Protein Donor)	false
O1N	N	THR- 191	2.74	163.01	H-Bond (Protein Donor)	false
O1N	OG1	THR- 191	2.9	173.22	H-Bond (Protein Donor)	false
O5D	OG1	THR- 191	3.4	121.34	H-Bond (Protein Donor)	false
O3B	OD2	ASP- 210	2.86	169.43	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 210	2.77	169.62	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 210	3.43	131.88	H-Bond (Ligand Donor)	false
C2B	CD1	TYR- 212	4	0	Hydrophobic	false
C3B	CD2	LEU- 213	4.48	0	Hydrophobic	false
C1B	CB	CYS- 243	3.94	0	Hydrophobic	false
C3D	CB	ASN- 244	4.4	0	Hydrophobic	false
N7A	ND2	ASN- 246	3.16	135.8	H-Bond (Protein Donor)	false
N7A	ND2	ASN- 249	3.21	130.48	H-Bond (Protein Donor)	false
N7N	O	ALA- 270	2.89	147.68	H-Bond (Ligand Donor)	false
C4D	CB	ALA- 271	4.45	0	Hydrophobic	false
N7N	OD2	ASP- 296	2.95	161.34	H-Bond (Ligand Donor)	false
O7N	N	TRP- 324	3.11	127.31	H-Bond (Protein Donor)	false
C4N	CB	TRP- 324	3.96	0	Hydrophobic	false
O1N	O	HOH- 925	2.85	172.15	H-Bond (Protein Donor)	false