scPDB - 4yxm entry

Protein Data Bank Entry:

PDB ID : 4yxm

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2015-03-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA integrity scanning protein DisA
ID:	DISA_THEMA
AC:	Q9WY43
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	50 %
B	50 %

Ligand binding site composition:

B-Factor:	45.763
Number of residues:	35
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.662	1667.250

% Hydrophobic	% Polar
31.98	68.02
According to VolSite

Ligand :

HET Code:	2BA
Formula:	C20H22N10O12P2
Molecular weight:	656.396 g/mol
DrugBank ID:	-
Buried Surface Area:	65.34 %
Polar Surface area:	334.95 Å2

Number of
H-Bond Acceptors:	20
H-Bond Donors:	4
Rings:	7
Aromatic rings:	4
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
13.8455	-36.9153	-39.6359

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
O1P	ND2	ASN- 75	2.85	124.22	H-Bond (Protein Donor)	false
O2P	ND2	ASN- 75	3.02	164.13	H-Bond (Protein Donor)	false
O2P1	ND2	ASN- 75	2.96	131.66	H-Bond (Protein Donor)	false
O2'1	OD1	ASN- 75	3.24	144.48	H-Bond (Ligand Donor)	false
O2'	N	GLY- 76	3.05	161.69	H-Bond (Protein Donor)	false
O2'1	N	GLY- 76	2.89	153.44	H-Bond (Protein Donor)	false
N6	O	LEU- 94	2.83	170.71	H-Bond (Ligand Donor)	false
N61	O	LEU- 94	2.91	175.69	H-Bond (Ligand Donor)	false
N1	N	LEU- 94	2.9	164.22	H-Bond (Protein Donor)	false
N11	N	LEU- 94	3.14	160.79	H-Bond (Protein Donor)	false
O1P	OG1	THR- 107	2.78	149.16	H-Bond (Protein Donor)	false
C2'	CG2	THR- 107	4.49	0	Hydrophobic	false
N6	OG1	THR- 111	3.04	126.29	H-Bond (Ligand Donor)	false
N61	OG1	THR- 111	3.01	124.39	H-Bond (Ligand Donor)	false