scPDB - 1p4a entry

Protein Data Bank Entry:

PDB ID : 1p4a

Resolution :2.220 Å

Experimental Method : X-ray

Deposition Date : 2003-04-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pur operon repressor
ID:	PURR_BACSU
AC:	P37551
Organism:	Bacillus subtilis
Reign:	Bacteria
TaxID:	224308
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	92 %
B	8 %

Ligand binding site composition:

B-Factor:	37.340
Number of residues:	26
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.184	762.750

% Hydrophobic	% Polar
35.84	64.16
According to VolSite

Ligand :

HET Code:	PCP
Formula:	C6H10O13P3
Molecular weight:	383.057 g/mol
DrugBank ID:	DB03942
Buried Surface Area:	67.98 %
Polar Surface area:	264.08 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	2
Rings:	1
Aromatic rings:	0
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
44.424	80.4199	62.0456

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
O2A	N	THR- 139	3.45	135.35	H-Bond (Protein Donor)	false
O1B	N	THR- 139	3.42	124.13	H-Bond (Protein Donor)	false
O2B	N	THR- 139	3.08	146.26	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 140	3.57	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 140	3.36	0	Ionic (Protein Cationic)	false
O3B	NZ	LYS- 140	2.75	0	Ionic (Protein Cationic)	false
O3A	NZ	LYS- 140	2.83	166.47	H-Bond (Protein Donor)	false
O2B	N	LYS- 140	2.6	156.41	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 140	3.36	127.96	H-Bond (Protein Donor)	false
O1B	NH2	ARG- 160	3.29	126.91	H-Bond (Protein Donor)	false
O3B	NH1	ARG- 160	2.77	138.71	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 160	3.24	124.8	H-Bond (Protein Donor)	false
O3B	CZ	ARG- 160	3.39	0	Ionic (Protein Cationic)	false
OP	N	GLY- 178	3.06	132.09	H-Bond (Protein Donor)	false
O1P	N	GLY- 178	3.42	150.99	H-Bond (Protein Donor)	false
C5	CB	SER- 179	4.33	0	Hydrophobic	false
O2	OD1	ASP- 203	2.71	142.64	H-Bond (Ligand Donor)	false
O2	OD2	ASP- 203	3	139.18	H-Bond (Ligand Donor)	false
O1A	OD2	ASP- 204	2.88	159.51	H-Bond (Protein Donor)	false
O3	O	PHE- 205	2.83	150.51	H-Bond (Ligand Donor)	false
CP	CB	LYS- 207	3.53	0	Hydrophobic	false
O2P	N	LYS- 207	3.1	126.33	H-Bond (Protein Donor)	false
O3P	N	ALA- 208	2.6	141.13	H-Bond (Protein Donor)	false
O2P	N	GLY- 209	2.97	148.79	H-Bond (Protein Donor)	false
O3P	N	GLY- 209	2.79	123.13	H-Bond (Protein Donor)	false
O3P	N	GLY- 210	3.37	144.84	H-Bond (Protein Donor)	false
C2	CG2	THR- 211	4.49	0	Hydrophobic	false
C3	CB	THR- 211	3.51	0	Hydrophobic	false
O1P	N	THR- 211	2.72	143.86	H-Bond (Protein Donor)	false