scPDB - 1iv2 entry

Protein Data Bank Entry:

PDB ID : 1iv2

Resolution :1.550 Å

Experimental Method : X-ray

Deposition Date : 2002-03-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
ID:	ISPF_THET8
AC:	Q8RQP5
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	4.6.1.12

Chains:

Chain Name:	Percentage of Residues within binding site
D	44 %
F	56 %

Ligand binding site composition:

B-Factor:	20.310
Number of residues:	34
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.838	840.375

% Hydrophobic	% Polar
42.97	57.03
According to VolSite

Ligand :

HET Code:	CDP
Formula:	C9H12N3O11P2
Molecular weight:	400.153 g/mol
DrugBank ID:	DB04555
Buried Surface Area:	65.84 %
Polar Surface area:	249.77 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-6.48588	42.9976	52.0299

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
O3'	O	HOH- 63	2.52	154.76	H-Bond (Protein Donor)	false
O2'	OD2	ASP- 1056	3.2	134.9	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 1056	2.65	163.7	H-Bond (Ligand Donor)	false
N4	O	LEU- 1500	2.92	172.51	H-Bond (Ligand Donor)	false
N4	O	PRO- 1503	3.1	146.52	H-Bond (Ligand Donor)	false
O2	N	LEU- 1505	3.35	123.38	H-Bond (Protein Donor)	false
N3	N	LEU- 1505	2.88	176.38	H-Bond (Protein Donor)	false
O2	N	GLY- 1506	2.83	140.64	H-Bond (Protein Donor)	false
C2'	CB	PHE- 1531	3.86	0	Hydrophobic	false
O1B	NZ	LYS- 1532	2.97	129.91	H-Bond (Protein Donor)	false
O3A	NZ	LYS- 1532	3	159	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 1532	2.97	0	Ionic (Protein Cationic)	false
O1A	OG1	THR- 1533	2.81	172.53	H-Bond (Protein Donor)	false
O1A	N	THR- 1533	2.76	153.89	H-Bond (Protein Donor)	false
O1B	MG	MG- 1564	1.92	0	Metal Acceptor	false
O3B	MG	MG- 1574	2.27	0	Metal Acceptor	false
O2A	MG	MG- 1574	2.26	0	Metal Acceptor	false