scPDB - 4wud entry

Protein Data Bank Entry:

PDB ID : 4wud

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2014-10-31

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 B
ID:	GYRB_ECOLI
AC:	P0AES6
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	36.224
Number of residues:	44
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.747	590.625

% Hydrophobic	% Polar
52.00	48.00
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	77.32 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
13.1214	19.6878	-11.9208

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
O1A	ND2	ASN- 46	3	145.55	H-Bond (Protein Donor)	false
N6	OD2	ASP- 73	2.83	152.9	H-Bond (Ligand Donor)	false
C1'	CG1	ILE- 78	4.49	0	Hydrophobic	false
C5'	CG2	ILE- 94	3.8	0	Hydrophobic	false
C4'	CG1	ILE- 94	4.01	0	Hydrophobic	false
C1'	CD1	ILE- 94	3.88	0	Hydrophobic	false
O3'	N	GLY- 102	2.97	164.47	H-Bond (Protein Donor)	false
O2'	N	GLY- 102	3.24	120.74	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 103	2.85	156.77	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 103	2.85	0	Ionic (Protein Cationic)	false
C3'	CD	LYS- 103	4.34	0	Hydrophobic	false
C2'	CE1	TYR- 109	4.17	0	Hydrophobic	false
O3G	N	LEU- 115	2.88	172.42	H-Bond (Protein Donor)	false
O3G	N	HIS- 116	3.12	172.84	H-Bond (Protein Donor)	false
O1G	N	VAL- 118	2.84	160.31	H-Bond (Protein Donor)	false
O1G	N	GLY- 119	2.88	145.32	H-Bond (Protein Donor)	false
O1A	N	VAL- 120	3.21	142.05	H-Bond (Protein Donor)	false
O2A	N	VAL- 120	3.05	147.95	H-Bond (Protein Donor)	false
O1G	NE2	GLN- 335	3.14	153.71	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 337	3.96	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 337	2.56	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 337	2.56	168.86	H-Bond (Protein Donor)	false
O2G	MG	MG- 402	2.04	0	Metal Acceptor	false
O2B	MG	MG- 402	2.12	0	Metal Acceptor	false
O1A	MG	MG- 402	2.22	0	Metal Acceptor	false