scPDB - 4jem entry

Protein Data Bank Entry:

PDB ID : 4jem

Resolution :1.550 Å

Experimental Method : X-ray

Deposition Date : 2013-02-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	CMP/hydroxymethyl CMP hydrolase
ID:	B4Y381_9ACTN
AC:	B4Y381
Organism:	Streptomyces rimofaciens
Reign:	Bacteria
TaxID:	504097
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	9 %
B	91 %

Ligand binding site composition:

B-Factor:	15.016
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.784	489.375

% Hydrophobic	% Polar
46.90	53.10
According to VolSite

Ligand :

HET Code:	C5P
Formula:	C9H12N3O8P
Molecular weight:	321.181 g/mol
DrugBank ID:	DB03403
Buried Surface Area:	78.84 %
Polar Surface area:	190.61 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
11.6047	21.5261	22.698

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
O3'	N	GLY- 20	2.98	157.05	H-Bond (Protein Donor)	false
O2P	N	PHE- 22	3.02	159.49	H-Bond (Protein Donor)	false
C5'	CB	PHE- 22	3.6	0	Hydrophobic	false
O1P	N	ARG- 23	2.91	169.2	H-Bond (Protein Donor)	false
C2'	CB	ALA- 58	3.59	0	Hydrophobic	false
N3	OE2	GLU- 62	2.84	150.26	H-Bond (Protein Donor)	false
O2	OE2	GLU- 62	3.34	128.84	H-Bond (Protein Donor)	false
N4	OE1	GLU- 62	2.95	146.81	H-Bond (Ligand Donor)	false
O2P	OG	SER- 97	2.51	156.31	H-Bond (Protein Donor)	false
O3P	N	GLY- 99	2.83	159.68	H-Bond (Protein Donor)	false
O3'	OE1	GLU- 103	2.67	167.41	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 103	3.39	147.5	H-Bond (Ligand Donor)	false
C1'	CD2	LEU- 127	3.95	0	Hydrophobic	false
O2P	O	HOH- 322	2.59	179.97	H-Bond (Protein Donor)	false
O2'	O	HOH- 331	2.87	154.83	H-Bond (Protein Donor)	false