scPDB - 3l0n entry

Protein Data Bank Entry:

PDB ID : 3l0n

Resolution :1.740 Å

Experimental Method : X-ray

Deposition Date : 2009-12-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uridine 5'-monophosphate synthase
ID:	UMPS_HUMAN
AC:	P11172
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	4.1.1.23

Chains:

Chain Name:	Percentage of Residues within binding site
A	13 %
B	87 %

Ligand binding site composition:

B-Factor:	23.939
Number of residues:	33
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.367	499.500

% Hydrophobic	% Polar
37.16	62.84
According to VolSite

Ligand :

HET Code:	S5P
Formula:	C9H10N2O9PS
Molecular weight:	353.222 g/mol
DrugBank ID:	-
Buried Surface Area:	79.68 %
Polar Surface area:	201.23 Å2

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

Mass center Coordinates

X	Y	Z
22.5398	-5.00205	14.1967

Binding mode :

What is Poseview ?

2D View
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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
C4'	CB	SER- 33	4.2	0	Hydrophobic	false
O3'	OD1	ASP- 35	3.41	126.31	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 35	2.71	165.85	H-Bond (Ligand Donor)	false
S22	CD	LYS- 57	4.26	0	Hydrophobic	false
O3'	NZ	LYS- 57	2.94	144.47	H-Bond (Protein Donor)	false
O2'	NE2	HIS- 59	3.19	137.6	H-Bond (Protein Donor)	false
O3'	NE2	HIS- 59	2.91	146.26	H-Bond (Protein Donor)	false
O2'	OD1	ASP- 93	2.7	168.56	H-Bond (Ligand Donor)	false
C5'	CD1	ILE- 94	4.39	0	Hydrophobic	false
C2'	CD1	ILE- 94	3.89	0	Hydrophobic	false
O2'	OG1	THR- 97	3.08	173.09	H-Bond (Protein Donor)	false
O4	N	SER- 148	2.97	158.75	H-Bond (Protein Donor)	false
N3	OG	SER- 148	2.74	146.27	H-Bond (Ligand Donor)	false
S22	CG2	ILE- 177	4.34	0	Hydrophobic	false
S22	CG	PRO- 193	4.25	0	Hydrophobic	false
C1'	CB	PRO- 193	4.14	0	Hydrophobic	false
O2	NE2	GLN- 206	2.96	135.29	H-Bond (Protein Donor)	false
O1P	NE2	GLN- 206	2.89	171.91	H-Bond (Protein Donor)	false
O1P	OH	TYR- 208	2.69	136.77	H-Bond (Protein Donor)	false
C4'	CG2	ILE- 224	4.4	0	Hydrophobic	false
O2P	N	GLY- 226	3.01	149.61	H-Bond (Protein Donor)	false
O3P	CZ	ARG- 227	3.67	0	Ionic (Protein Cationic)	false
O1P	CZ	ARG- 227	3.69	0	Ionic (Protein Cationic)	false
O3P	NE	ARG- 227	2.75	167.22	H-Bond (Protein Donor)	false
O3P	N	ARG- 227	2.78	170.02	H-Bond (Protein Donor)	false
O1P	NH2	ARG- 227	2.89	156.62	H-Bond (Protein Donor)	false
O2P	O	HOH- 259	2.51	150.68	H-Bond (Protein Donor)	false
O2P	O	HOH- 296	2.74	179.97	H-Bond (Protein Donor)	false