scPDB - 3nwy entry

Protein Data Bank Entry:

PDB ID : 3nwy

Resolution :2.540 Å

Experimental Method : X-ray

Deposition Date : 2010-07-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uridylate kinase
ID:	PYRH_MYCTU
AC:	P9WHK5
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	59 %
C	33 %
E	4 %
F	4 %

Ligand binding site composition:

B-Factor:	37.072
Number of residues:	28
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:	GTP GTP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.060	1366.875

% Hydrophobic	% Polar
45.93	54.07
According to VolSite

Ligand :

HET Code:	GTP
Formula:	C10H12N5O14P3
Molecular weight:	519.149 g/mol
DrugBank ID:	DB04137
Buried Surface Area:	52.09 %
Polar Surface area:	335.56 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
80.8617	33.3758	53.6587

Binding mode :

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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
O1B	NH1	ARG- 123	2.55	164.45	H-Bond (Protein Donor)	false
O1B	NH2	ARG- 123	3.15	128.83	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 123	3.27	0	Ionic (Protein Cationic)	false
C2'	CD	ARG- 123	4.42	0	Hydrophobic	false
N1	O	GLY- 131	2.87	143.55	H-Bond (Ligand Donor)	false
N2	O	GLY- 131	3.01	138.74	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 135	3.44	151.16	H-Bond (Ligand Donor)	false
C1'	CB	LEU- 140	3.95	0	Hydrophobic	false
C4'	CB	LEU- 140	3.78	0	Hydrophobic	false
O1A	CZ	ARG- 141	3.98	0	Ionic (Protein Cationic)	false
O2A	NH2	ARG- 141	3.43	149.39	H-Bond (Protein Donor)	false
O2G	NH2	ARG- 144	3.26	127.92	H-Bond (Protein Donor)	false
C5'	CG	ARG- 144	4.21	0	Hydrophobic	false
O1G	NZ	LYS- 148	3.71	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 148	3.49	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 148	3.28	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 148	3.49	172.8	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 150	3.74	0	Ionic (Protein Cationic)	false
O2B	NH2	ARG- 150	3.21	126.14	H-Bond (Protein Donor)	false