scPDB - 4fdu entry

Protein Data Bank Entry:

PDB ID : 4fdu

Resolution :2.290 Å

Experimental Method : X-ray

Deposition Date : 2012-05-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative multiple inositol polyphosphate histidine phosphatase 1
ID:	Q89YI8_BACTN
AC:	Q89YI8
Organism:	Bacteroides thetaiotaomicron
Reign:	Bacteria
TaxID:	226186
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	36.459
Number of residues:	29
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.036	941.625

% Hydrophobic	% Polar
27.60	72.40
According to VolSite

Ligand :

HET Code:	IHS
Formula:	C6H6O24S6
Molecular weight:	654.487 g/mol
DrugBank ID:	DB01666
Buried Surface Area:	50.52 %
Polar Surface area:	448.86 Å2

Number of
H-Bond Acceptors:	24
H-Bond Donors:	0
Rings:	1
Aromatic rings:	0
Anionic atoms:	6
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
26.006	19.0086	35.0786

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
O24	OG1	THR- 30	2.8	164.17	H-Bond (Protein Donor)	false
O23	NH2	ARG- 58	3.5	124.49	H-Bond (Protein Donor)	false
O23	NE	ARG- 58	3.18	132.54	H-Bond (Protein Donor)	false
O33	NH2	ARG- 58	2.85	157.18	H-Bond (Protein Donor)	false
O23	CZ	ARG- 58	3.72	0	Ionic (Protein Cationic)	false
O33	CZ	ARG- 58	3.84	0	Ionic (Protein Cationic)	false
O14	NH2	ARG- 62	3.42	136.19	H-Bond (Protein Donor)	false
O25	NH2	ARG- 62	3.39	131.51	H-Bond (Protein Donor)	false
O33	NE	ARG- 62	2.81	154.99	H-Bond (Protein Donor)	false
O33	NH2	ARG- 62	3.33	130.17	H-Bond (Protein Donor)	false
O33	CZ	ARG- 62	3.49	0	Ionic (Protein Cationic)	false
C1	CG2	THR- 65	4.38	0	Hydrophobic	false
O2	OG1	THR- 65	3.17	147.34	H-Bond (Protein Donor)	false
O4	NH2	ARG- 149	3.43	147.72	H-Bond (Protein Donor)	false
O43	NE	ARG- 149	2.95	144.68	H-Bond (Protein Donor)	false
O43	NH2	ARG- 149	2.99	140.84	H-Bond (Protein Donor)	false
O43	CZ	ARG- 149	3.38	0	Ionic (Protein Cationic)	false
O22	CZ	ARG- 183	3.23	0	Ionic (Protein Cationic)	false
O22	NH2	ARG- 183	2.72	120.49	H-Bond (Protein Donor)	false
O42	NH1	ARG- 183	3.32	154.89	H-Bond (Protein Donor)	false
O26	NZ	LYS- 195	3.67	0	Ionic (Protein Cationic)	false
O44	NE2	GLN- 276	3.31	165.45	H-Bond (Protein Donor)	false
O34	NZ	LYS- 280	3.28	133.43	H-Bond (Protein Donor)	false
O34	NZ	LYS- 280	3.28	0	Ionic (Protein Cationic)	false
O44	NZ	LYS- 280	3.36	0	Ionic (Protein Cationic)	false
O43	ND1	HIS- 323	3.03	164.75	H-Bond (Protein Donor)	false
O23	N	ALA- 324	2.67	174.53	H-Bond (Protein Donor)	false
O12	OE1	GLU- 325	2.85	147.61	H-Bond (Protein Donor)	false
O13	OE1	GLU- 325	3.27	133.5	H-Bond (Protein Donor)	false