scPDB - 1zny entry

Protein Data Bank Entry:

PDB ID : 1zny

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2005-05-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Guanylate kinase
ID:	KGUA_MYCTU
AC:	P9WKE9
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	2.7.4.8

Chains:

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

Ligand binding site composition:

B-Factor:	24.232
Number of residues:	22
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.046	381.375

% Hydrophobic	% Polar
30.09	69.91
According to VolSite

Ligand :

HET Code:	GDP
Formula:	C10H12N5O11P2
Molecular weight:	440.177 g/mol
DrugBank ID:	DB04315
Buried Surface Area:	37.74 %
Polar Surface area:	276.39 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
25.7164	8.15311	31.7074

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
O6	OG	SER- 53	2.65	167.35	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 57	2.98	153.23	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 60	3.42	167.07	H-Bond (Protein Donor)	false
O1A	OH	TYR- 69	3	139.24	H-Bond (Protein Donor)	false
N1	OE1	GLU- 88	2.72	157.58	H-Bond (Ligand Donor)	false
N1	OE2	GLU- 88	3.34	131.4	H-Bond (Ligand Donor)	false
N2	OE2	GLU- 88	2.77	155.62	H-Bond (Ligand Donor)	false
C4'	CG2	ILE- 92	4.07	0	Hydrophobic	false
C1'	CD1	ILE- 92	3.83	0	Hydrophobic	false