scPDB - 3zgn entry

Protein Data Bank Entry:

PDB ID : 3zgn

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2012-12-18

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
B	100 %

Ligand binding site composition:

B-Factor:	20.533
Number of residues:	32
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.895	405.000

% Hydrophobic	% Polar
50.00	50.00
According to VolSite

Ligand :

HET Code:	10G
Formula:	C5H9O7P2S
Molecular weight:	275.133 g/mol
DrugBank ID:	-
Buried Surface Area:	79.58 %
Polar Surface area:	180.2 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	1
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
16.3071	2.22467	-4.16273

Binding mode :

What is Poseview ?

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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
C6	CG2	VAL- 15	3.54	0	Hydrophobic	false
C4	CG2	VAL- 15	4.08	0	Hydrophobic	false
C4	CG1	VAL- 40	4.25	0	Hydrophobic	false
O10	N	HIS- 41	2.74	178.62	H-Bond (Protein Donor)	false
C4	CB	ALA- 73	3.4	0	Hydrophobic	false
C1	CB	ALA- 73	4.4	0	Hydrophobic	false
O11	NE2	HIS- 74	3.45	122.06	H-Bond (Protein Donor)	false
O10	NE2	HIS- 74	3.11	146.26	H-Bond (Protein Donor)	false
C1	CB	HIS- 74	4.37	0	Hydrophobic	false
S2	CG2	VAL- 99	3.52	0	Hydrophobic	false
O13	NE2	HIS- 124	2.92	164.67	H-Bond (Protein Donor)	false
S2	CB	THR- 167	4.43	0	Hydrophobic	false
S2	CG2	THR- 168	4.46	0	Hydrophobic	false
O9	OG	SER- 225	2.63	160.44	H-Bond (Protein Donor)	false
O13	N	SER- 226	2.8	166.7	H-Bond (Protein Donor)	false
O14	N	ASN- 227	2.92	174.47	H-Bond (Protein Donor)	false
O14	ND2	ASN- 227	2.76	147.14	H-Bond (Protein Donor)	false
C6	CB	ALA- 268	4.35	0	Hydrophobic	false
O9	OG	SER- 269	2.9	157.14	H-Bond (Protein Donor)	false
C6	CB	SER- 269	4.36	0	Hydrophobic	false
O15	O	HOH- 2119	2.51	149.54	H-Bond (Protein Donor)	false