scPDB - 3dh7 entry

Protein Data Bank Entry:

PDB ID : 3dh7

Resolution :2.970 Å

Experimental Method : X-ray

Deposition Date : 2008-06-17

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:	Q53W52_THET8
AC:	Q53W52
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	16.184
Number of residues:	46
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.555	887.625

% Hydrophobic	% Polar
41.44	58.56
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	75.76 %
Polar Surface area:	217.05 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
46.006	-45.2847	-38.3657

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
C7M	CD2	LEU- 11	3.82	0	Hydrophobic	false
C8M	SG	CYS- 14	3.47	0	Hydrophobic	false
C8	CG	MET- 66	3.44	0	Hydrophobic	false
O4	N	SER- 95	3.39	166.64	H-Bond (Protein Donor)	false
N3	OD1	ASN- 123	3.28	132.17	H-Bond (Ligand Donor)	false
O2	NZ	LYS- 187	2.82	129.05	H-Bond (Protein Donor)	false
O2'	NZ	LYS- 187	2.96	153.91	H-Bond (Protein Donor)	false
C5'	CG2	THR- 217	3.76	0	Hydrophobic	false
O2P	N	THR- 217	2.97	159.99	H-Bond (Protein Donor)	false
C7M	CH2	TRP- 219	4.33	0	Hydrophobic	false
C8M	CZ2	TRP- 219	3.59	0	Hydrophobic	false
C1'	CE2	TRP- 219	4.04	0	Hydrophobic	false
C9	CZ2	TRP- 219	2.97	0	Hydrophobic	false
O2P	N	GLY- 264	3.21	131.27	H-Bond (Protein Donor)	false
O2P	OH	TYR- 266	2.58	138.86	H-Bond (Protein Donor)	false
O3P	OH	TYR- 266	3.01	125.28	H-Bond (Protein Donor)	false
C5'	CB	ALA- 285	4.24	0	Hydrophobic	false
C2'	CB	ALA- 285	3.64	0	Hydrophobic	false
O3P	N	ALA- 285	3.28	156.73	H-Bond (Protein Donor)	false
C8M	CB	ARG- 286	3.76	0	Hydrophobic	false
O3P	N	ARG- 286	3.24	124.89	H-Bond (Protein Donor)	false
C7M	CD2	LEU- 289	3.82	0	Hydrophobic	false
C8M	CD2	LEU- 289	3.98	0	Hydrophobic	false
O3P	O	HOH- 1115	3.32	170.46	H-Bond (Protein Donor)	false