scPDB - 1jkx entry

Protein Data Bank Entry:

PDB ID : 1jkx

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2001-07-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phosphoribosylglycinamide formyltransferase
ID:	PUR3_ECOLI
AC:	P08179
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	28.555
Number of residues:	55
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.144	877.500

% Hydrophobic	% Polar
40.77	59.23
According to VolSite

Ligand :

HET Code:	138
Formula:	C30H34N6O15P
Molecular weight:	749.596 g/mol
DrugBank ID:	DB02794
Buried Surface Area:	49.22 %
Polar Surface area:	379.25 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	8
Rings:	4
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	17

Mass center Coordinates

X	Y	Z
17.8927	62.0031	21.3272

Binding mode :

What is Poseview ?

2D View
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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
O32	N	GLY- 11	2.76	153.7	H-Bond (Protein Donor)	false
O31	OG	SER- 12	2.63	160.31	H-Bond (Protein Donor)	false
O31	N	SER- 12	2.92	158.28	H-Bond (Protein Donor)	false
O30	N	ASN- 13	3.02	161.61	H-Bond (Protein Donor)	false
O30	ND2	ASN- 13	2.98	152.67	H-Bond (Protein Donor)	false
O	NH2	ARG- 64	3.4	143.66	H-Bond (Protein Donor)	false
O	NH1	ARG- 64	3.19	154.78	H-Bond (Protein Donor)	false
OT	NH2	ARG- 64	2.86	146.41	H-Bond (Protein Donor)	false
O	CZ	ARG- 64	3.75	0	Ionic (Protein Cationic)	false
OT	CZ	ARG- 64	3.92	0	Ionic (Protein Cationic)	false
C8	CD1	LEU- 85	4.47	0	Hydrophobic	false
C16	CB	MET- 89	3.98	0	Hydrophobic	false
C15	CE	MET- 89	3.8	0	Hydrophobic	false
N	O	MET- 89	3.12	161.84	H-Bond (Ligand Donor)	false
OT	N	ILE- 91	2.74	158.75	H-Bond (Protein Donor)	false
C12	CG1	ILE- 91	3.56	0	Hydrophobic	false
N1	N	LEU- 92	3.13	162.03	H-Bond (Protein Donor)	false
NA2	O	LEU- 92	2.89	152.67	H-Bond (Ligand Donor)	false
C8	CG	LEU- 92	4.24	0	Hydrophobic	false
C23	CG2	ILE- 107	3.96	0	Hydrophobic	false
C15	CD2	LEU- 118	4.15	0	Hydrophobic	false
O24	OE1	GLU- 173	2.57	123.78	H-Bond (Ligand Donor)	false
O24	OE2	GLU- 173	2.73	161.58	H-Bond (Ligand Donor)	false
O30	O	HOH- 4224	2.72	165.23	H-Bond (Protein Donor)	false
N21	O	HOH- 4230	2.97	151.33	H-Bond (Ligand Donor)	false