scPDB - 1w4a entry

Protein Data Bank Entry:

PDB ID : 1w4a

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2004-07-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NTPase P4
ID:	Q94M05_9VIRU
AC:	Q94M05
Organism:	Pseudomonas phage phi12
Reign:	Viruses
TaxID:	161736
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	34 %
C	66 %

Ligand binding site composition:

B-Factor:	29.249
Number of residues:	44
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	8
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.598	499.500

% Hydrophobic	% Polar
42.57	57.43
According to VolSite

Ligand :

HET Code:	APC
Formula:	C11H14N5O12P3
Molecular weight:	501.176 g/mol
DrugBank ID:	DB02596
Buried Surface Area:	56.8 %
Polar Surface area:	310.64 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	3
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
31.9842	52.5093	27.2272

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
O2B	N	THR- 137	2.92	142.98	H-Bond (Protein Donor)	false
C3A	CB	THR- 137	3.61	0	Hydrophobic	false
C5'	CG	PRO- 138	4.18	0	Hydrophobic	false
O1G	NZ	LYS- 192	2.9	129.31	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 192	2.9	0	Ionic (Protein Cationic)	false
C2'	CG	GLN- 278	4.22	0	Hydrophobic	false
C1'	CZ	TYR- 288	4.06	0	Hydrophobic	false
DuAr	DuAr	TYR- 288	3.49	0	Aromatic Face/Face	false
O1B	NZ	LYS- 310	3.56	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 310	2.77	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 310	2.77	169.51	H-Bond (Protein Donor)	false
C3'	CD	LYS- 310	4.23	0	Hydrophobic	false
N6	O	HOH- 2175	2.76	125.18	H-Bond (Ligand Donor)	false
O1A	O	HOH- 2191	2.7	153.09	H-Bond (Protein Donor)	false
O2'	O	HOH- 2192	2.79	152.6	H-Bond (Ligand Donor)	false
O2A	O	HOH- 2196	3.22	158.63	H-Bond (Protein Donor)	false