scPDB - 2y3p entry

Protein Data Bank Entry:

PDB ID : 2y3p

Resolution :2.620 Å

Experimental Method : X-ray

Deposition Date : 2010-12-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA gyrase subunit A
ID:	GYRA_SHIFL
AC:	P0AES5
Organism:	Shigella flexneri
Reign:	Bacteria
TaxID:	623
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	93 %
B	7 %

Ligand binding site composition:

B-Factor:	34.426
Number of residues:	31
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.016	371.250

% Hydrophobic	% Polar
39.09	60.91
According to VolSite

Ligand :

HET Code:	SM8
Formula:	C46H41ClNO18
Molecular weight:	931.267 g/mol
DrugBank ID:	-
Buried Surface Area:	25.52 %
Polar Surface area:	308.34 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	7
Rings:	8
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-7.56064	50.8283	29.374

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
C4F	CD2	LEU- 41	3.96	0	Hydrophobic	false
O3B	NZ	LYS- 42	2.68	147.72	H-Bond (Protein Donor)	false
O3B	NE2	HIS- 45	3.47	151.83	H-Bond (Protein Donor)	false
DuAr	DuAr	HIS- 45	3.53	0	Aromatic Face/Face	false
C4E	CB	HIS- 45	4.04	0	Hydrophobic	false
C4D	CG2	THR- 88	4.35	0	Hydrophobic	false
O4A	NE	ARG- 91	3.29	168.14	H-Bond (Protein Donor)	false
C4D	CG	MET- 92	3.45	0	Hydrophobic	false
C4C	CD1	LEU- 98	4.22	0	Hydrophobic	false
C4G	CD1	LEU- 98	3.91	0	Hydrophobic	false
C4F	CD2	LEU- 98	4.04	0	Hydrophobic	false
C4F	CD1	LEU- 102	3.94	0	Hydrophobic	false
O4B	ND2	ASN- 165	3.35	158.03	H-Bond (Protein Donor)	false
CL4	CB	ASN- 169	3.77	0	Hydrophobic	false
O1A	MG	MG- 951	2.49	0	Metal Acceptor	false
O1B	MG	MG- 951	2.35	0	Metal Acceptor	false
O1D	MG	MG- 952	2.48	0	Metal Acceptor	false
O1F	MG	MG- 952	2.44	0	Metal Acceptor	false