scPDB - 2cu0 entry

Protein Data Bank Entry:

PDB ID : 2cu0

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2005-05-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Inosine-5'-monophosphate dehydrogenase
ID:	IMDH_PYRHO
AC:	O58045
Organism:	Pyrococcus horikoshii
Reign:	Archaea
TaxID:	70601
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	34.699
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.108	1184.625

% Hydrophobic	% Polar
42.74	57.26
According to VolSite

Ligand :

HET Code:	XMP
Formula:	C10H11N4O9P
Molecular weight:	362.190 g/mol
DrugBank ID:	DB02309
Buried Surface Area:	67.31 %
Polar Surface area:	207.94 Å2

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

Mass center Coordinates

X	Y	Z
24.8726	-1.79446	49.5492

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
C3'	CB	ALA- 53	3.97	0	Hydrophobic	false
C5'	SD	MET- 55	4.21	0	Hydrophobic	false
C3'	SD	MET- 55	3.81	0	Hydrophobic	false
O1P	N	SER- 299	2.88	151.23	H-Bond (Protein Donor)	false
O3P	OG	SER- 299	2.77	162.45	H-Bond (Protein Donor)	false
O2	OG1	THR- 303	2.68	139.73	H-Bond (Protein Donor)	false
O2'	OD2	ASP- 334	2.96	143.95	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 334	2.87	122.08	H-Bond (Ligand Donor)	false
O1P	N	GLY- 336	2.96	154.38	H-Bond (Protein Donor)	false
O2P	N	GLY- 357	2.74	146.83	H-Bond (Protein Donor)	false
O2P	N	ASN- 358	3.19	145.29	H-Bond (Protein Donor)	false
O3P	N	ASN- 358	3.1	147.13	H-Bond (Protein Donor)	false
O3P	OH	TYR- 381	2.55	145.57	H-Bond (Protein Donor)	false
N7	N	MET- 384	2.98	150.55	H-Bond (Protein Donor)	false
O6	N	GLY- 385	2.7	141.11	H-Bond (Protein Donor)	false
N1	O	GLU- 412	2.87	129.9	H-Bond (Ligand Donor)	false
O2P	O	HOH- 1005	2.84	179.95	H-Bond (Protein Donor)	false
O2P	O	HOH- 1020	2.71	174.21	H-Bond (Protein Donor)	false