scPDB - 1xcb entry

Protein Data Bank Entry:

PDB ID : 1xcb

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2004-09-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Redox-sensing transcriptional repressor Rex
ID:	REX_THEAQ
AC:	Q9X2V5
Organism:	Thermus aquaticus
Reign:	Bacteria
TaxID:	271
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	6 %
G	94 %

Ligand binding site composition:

B-Factor:	22.861
Number of residues:	35
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.380	529.875

% Hydrophobic	% Polar
54.78	45.22
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	59.16 %
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
77.1001	85.2282	45.8375

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
C2B	CE1	PHE- 43	4.42	0	Hydrophobic	false
N7A	NH2	ARG- 46	3.35	152.1	H-Bond (Protein Donor)	false
O1A	N	ARG- 90	2.98	171.48	H-Bond (Protein Donor)	false
O1A	NE	ARG- 90	3.19	126.61	H-Bond (Protein Donor)	false
O3	NH2	ARG- 90	3.32	154.04	H-Bond (Protein Donor)	false
O1N	NH2	ARG- 90	2.87	131.81	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 90	3.97	0	Ionic (Protein Cationic)	false
O1N	CZ	ARG- 90	3.59	0	Ionic (Protein Cationic)	false
O2N	N	LEU- 91	2.68	171.49	H-Bond (Protein Donor)	false
C1D	CD1	LEU- 91	4.18	0	Hydrophobic	false
C5N	CD1	LEU- 91	3.55	0	Hydrophobic	false
O3B	OD2	ASP- 112	2.86	159.92	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 112	2.65	169.41	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 112	3.45	133.58	H-Bond (Ligand Donor)	false
N3A	N	VAL- 113	3.5	127.48	H-Bond (Protein Donor)	false
C1B	CG1	VAL- 148	4.34	0	Hydrophobic	false
N7N	O	PHE- 171	3.23	137.17	H-Bond (Ligand Donor)	false
N7N	O	VAL- 187	3.19	151.92	H-Bond (Ligand Donor)	false