scPDB - 4h8a entry

Protein Data Bank Entry:

PDB ID : 4h8a

Resolution :1.640 Å

Experimental Method : X-ray

Deposition Date : 2012-09-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ureidoglycolate dehydrogenase (NAD(+))
ID:	ALLD_ECOLI
AC:	P77555
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	1.1.1.350

Chains:

Chain Name:	Percentage of Residues within binding site
A	12 %
B	88 %

Ligand binding site composition:

B-Factor:	30.468
Number of residues:	54
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.177	1410.750

% Hydrophobic	% Polar
46.17	53.83
According to VolSite

Ligand :

HET Code:	NAI
Formula:	C21H27N7O14P2
Molecular weight:	663.425 g/mol
DrugBank ID:	DB00157
Buried Surface Area:	63.5 %
Polar Surface area:	342.9 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	6
Rings:	5
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
34.5134	1.52607	-11.0516

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
C4D	CG2	ILE- 41	4.14	0	Hydrophobic	false
N7N	O	GLY- 118	2.84	156.55	H-Bond (Ligand Donor)	false
O2D	N	ILE- 120	3.44	155.55	H-Bond (Protein Donor)	false
O7N	OG	SER- 140	3.16	154.6	H-Bond (Protein Donor)	false
C4N	CB	SER- 140	4.31	0	Hydrophobic	false
C4N	CB	THR- 156	4.16	0	Hydrophobic	false
C2D	CB	PRO- 158	3.89	0	Hydrophobic	false
C4N	CG	PRO- 158	3.73	0	Hydrophobic	false
C3B	CD1	PHE- 173	4.29	0	Hydrophobic	false
C4B	CE1	PHE- 173	3.59	0	Hydrophobic	false
O3B	N	ASP- 174	3.11	148.68	H-Bond (Protein Donor)	false
C3D	CB	ASP- 174	4.47	0	Hydrophobic	false
O2D	OD1	ASP- 174	2.81	136.02	H-Bond (Ligand Donor)	false
O2D	OD2	ASP- 174	3.06	159.58	H-Bond (Ligand Donor)	false
C5B	CB	MET- 175	4.34	0	Hydrophobic	false
O1N	N	ALA- 176	2.96	156.07	H-Bond (Protein Donor)	false
C5D	CB	ALA- 176	4.17	0	Hydrophobic	false
C5D	CB	ALA- 181	4.19	0	Hydrophobic	false
C1B	CB	PRO- 223	4.25	0	Hydrophobic	false
C5B	CG	LYS- 224	4.47	0	Hydrophobic	false
O1N	NZ	LYS- 224	3.19	139.19	H-Bond (Protein Donor)	false
O1N	NZ	LYS- 224	3.19	0	Ionic (Protein Cationic)	false
N3A	N	GLY- 306	3.37	153.89	H-Bond (Protein Donor)	false
O2B	OD1	ASP- 308	2.89	161.04	H-Bond (Ligand Donor)	false
O1A	O	HOH- 544	3.18	179.96	H-Bond (Protein Donor)	false
N1A	O	HOH- 544	2.85	179.97	H-Bond (Protein Donor)	false
O2A	O	HOH- 712	3.26	179.95	H-Bond (Protein Donor)	false
O2N	O	HOH- 798	2.75	179.95	H-Bond (Protein Donor)	false