scPDB - 3b04 entry

Protein Data Bank Entry:

PDB ID : 3b04

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2011-06-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Isopentenyl-diphosphate delta-isomerase
ID:	IDI2_SULSH
AC:	P61615
Organism:	Sulfolobus shibatae
Reign:	Archaea
TaxID:	2286
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	31.109
Number of residues:	60
Including
Standard Amino Acids:	54
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.081	729.000

% Hydrophobic	% Polar
35.65	64.35
According to VolSite

Ligand :

HET Code:	OOP
Formula:	C23H31N4O17P3
Molecular weight:	728.430 g/mol
DrugBank ID:	-
Buried Surface Area:	76.48 %
Polar Surface area:	379.96 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	7
Rings:	3
Aromatic rings:	1
Anionic atoms:	5
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
60.1375	18.9526	14.8466

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
O1B	NH2	ARG- 7	3.4	123.37	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 8	3.81	0	Ionic (Protein Cationic)	false
O3B	NZ	LYS- 8	2.68	0	Ionic (Protein Cationic)	false
O3B	NZ	LYS- 8	2.68	162.6	H-Bond (Protein Donor)	false
C7M	CG2	VAL- 12	4.07	0	Hydrophobic	false
C7M	CB	ALA- 15	4.2	0	Hydrophobic	false
C8M	CB	ALA- 15	4.11	0	Hydrophobic	false
O2'	OG1	THR- 65	2.84	166.45	H-Bond (Protein Donor)	false
O2'	O	GLY- 66	2.58	160.47	H-Bond (Ligand Donor)	false
N5	O	MET- 67	2.94	123.72	H-Bond (Ligand Donor)	false
C7M	CB	MET- 67	4.35	0	Hydrophobic	false
C8M	SD	MET- 67	4.17	0	Hydrophobic	false
C6	CB	MET- 67	3.98	0	Hydrophobic	false
C8	CG	MET- 67	3.7	0	Hydrophobic	false
O4	N	SER- 96	2.85	140.91	H-Bond (Protein Donor)	false
O2B	OG	SER- 96	3.24	132.26	H-Bond (Protein Donor)	false
O3B	OG	SER- 96	2.86	155.72	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 98	3.56	0	Ionic (Protein Cationic)	false
O1B	NH1	ARG- 98	2.66	160.12	H-Bond (Protein Donor)	false
O2	ND2	ASN- 125	2.98	164.22	H-Bond (Protein Donor)	false
N3	OD1	ASN- 125	3.21	163.08	H-Bond (Ligand Donor)	false
O15	OE1	GLN- 160	3.29	160	H-Bond (Ligand Donor)	false
O2	NZ	LYS- 193	2.69	169.64	H-Bond (Protein Donor)	false
O2'	NZ	LYS- 193	3.18	160.66	H-Bond (Protein Donor)	false
O3'	NZ	LYS- 193	3.31	124.01	H-Bond (Protein Donor)	false
C1'	CB	SER- 195	4.1	0	Hydrophobic	false
C14	CB	SER- 195	4.42	0	Hydrophobic	false
O3'	OG	SER- 218	2.98	169.45	H-Bond (Protein Donor)	false
O2P	N	THR- 223	3.1	163.93	H-Bond (Protein Donor)	false
O3P	OG1	THR- 223	2.6	161.42	H-Bond (Protein Donor)	false
C8M	CG2	THR- 223	4.19	0	Hydrophobic	false
C8M	CZ2	TRP- 225	4.08	0	Hydrophobic	false
C7	CZ2	TRP- 225	3.36	0	Hydrophobic	false
O2P	N	GLY- 275	2.84	162.5	H-Bond (Protein Donor)	false
O1P	NH2	ARG- 277	3.05	152.69	H-Bond (Protein Donor)	false
O2P	NH1	ARG- 277	2.93	154.54	H-Bond (Protein Donor)	false
O2P	NH2	ARG- 277	3.37	133.55	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 277	3.94	0	Ionic (Protein Cationic)	false
O2P	CZ	ARG- 277	3.58	0	Ionic (Protein Cationic)	false
O1P	N	ALA- 296	2.88	146	H-Bond (Protein Donor)	false
C3'	CB	ALA- 296	3.64	0	Hydrophobic	false
O3P	N	LEU- 297	3.14	168.04	H-Bond (Protein Donor)	false
C8M	CD1	LEU- 297	4.13	0	Hydrophobic	false
C7M	CD1	LEU- 300	4.17	0	Hydrophobic	false
O1P	O	HOH- 374	2.7	179.95	H-Bond (Protein Donor)	false
O3B	O	HOH- 394	2.53	179.95	H-Bond (Protein Donor)	false
O3'	O	HOH- 401	2.51	153.07	H-Bond (Ligand Donor)	false
O1A	MG	MG- 1002	2.2	0	Metal Acceptor	false