scPDB - 3kem entry

Protein Data Bank Entry:

PDB ID : 3kem

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2009-10-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	4-hydroxy-3-methylbut-2-enyl diphosphate reductase
ID:	ISPH_ECOLI
AC:	P62623
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	11.147
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.639	374.625

% Hydrophobic	% Polar
40.54	59.46
According to VolSite

Ligand :

HET Code:	IPE
Formula:	C5H9O7P2
Molecular weight:	243.068 g/mol
DrugBank ID:	DB04714
Buried Surface Area:	76.31 %
Polar Surface area:	141.4 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	0
Rings:	0
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
13.2056	-18.2396	30.8694

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
C1	CG2	VAL- 15	3.74	0	Hydrophobic	false
O1A	N	HIS- 41	2.71	169.36	H-Bond (Protein Donor)	false
O3B	ND1	HIS- 41	2.98	145.17	H-Bond (Protein Donor)	false
C4	CB	ALA- 73	3.65	0	Hydrophobic	false
O1A	NE2	HIS- 74	3.23	144.82	H-Bond (Protein Donor)	false
O3A	NE2	HIS- 74	3.17	120.98	H-Bond (Protein Donor)	false
C4	CB	CYS- 96	4.29	0	Hydrophobic	false
C4	CG2	VAL- 99	4.42	0	Hydrophobic	false
O3B	NE2	HIS- 124	2.77	172.38	H-Bond (Protein Donor)	false
C2	CG2	THR- 168	4.04	0	Hydrophobic	false
O2A	OG	SER- 225	2.58	153.28	H-Bond (Protein Donor)	false
O3B	N	SER- 226	2.62	153.35	H-Bond (Protein Donor)	false
O1B	N	ASN- 227	2.93	171.26	H-Bond (Protein Donor)	false
O1B	ND2	ASN- 227	2.58	155.35	H-Bond (Protein Donor)	false
O2A	OG	SER- 269	2.74	159.7	H-Bond (Protein Donor)	false
O2B	O	HOH- 328	2.55	144.74	H-Bond (Protein Donor)	false