scPDB - 2yqj entry

Protein Data Bank Entry:

PDB ID : 2yqj

Resolution :2.310 Å

Experimental Method : X-ray

Deposition Date : 2007-03-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-N-acetylglucosamine pyrophosphorylase
ID:	UAP1_CANAX
AC:	O74933
Organism:	Candida albicans
Reign:	Eukaryota
TaxID:	5476
EC Number:	2.7.7.23

Chains:

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

Ligand binding site composition:

B-Factor:	19.350
Number of residues:	49
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.903	1441.125

% Hydrophobic	% Polar
31.62	68.38
According to VolSite

Ligand :

HET Code:	UD1
Formula:	C17H25N3O17P2
Molecular weight:	605.338 g/mol
DrugBank ID:	DB03397
Buried Surface Area:	70.54 %
Polar Surface area:	325.69 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
11.7414	-4.63731	22.7439

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
C1B	CB	MET- 109	3.87	0	Hydrophobic	false
O2'	O	MET- 109	3.21	176.68	H-Bond (Ligand Donor)	false
O2	N	GLY- 111	2.85	144.18	H-Bond (Protein Donor)	false
O2'	N	GLY- 112	3.18	147.6	H-Bond (Protein Donor)	false
O1B	NH2	ARG- 116	2.86	157.69	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 116	3.89	0	Ionic (Protein Cationic)	false
N3	OE1	GLN- 199	2.62	163.21	H-Bond (Ligand Donor)	false
O4	NE2	GLN- 199	3.12	133.02	H-Bond (Protein Donor)	false
O7'	ND2	ASN- 227	2.59	151.21	H-Bond (Protein Donor)	false
O4B	ND2	ASN- 227	3.36	151.49	H-Bond (Protein Donor)	false
C1B	CB	ASN- 227	4.11	0	Hydrophobic	false
C5B	SG	CYS- 255	3.89	0	Hydrophobic	false
C3B	SG	CYS- 255	3.29	0	Hydrophobic	false
O3B	N	VAL- 256	3.18	148.08	H-Bond (Protein Donor)	false
C6'	CG1	VAL- 293	4.35	0	Hydrophobic	false
O3'	N	GLY- 294	3.3	131.89	H-Bond (Protein Donor)	false
O4'	N	GLY- 294	2.89	148.05	H-Bond (Protein Donor)	false
N2'	OE2	GLU- 309	2.67	168.57	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 309	2.81	158.24	H-Bond (Ligand Donor)	false
O2B	OH	TYR- 310	2.74	168	H-Bond (Protein Donor)	false
C4'	CB	ASN- 335	4.25	0	Hydrophobic	false
O3'	ND2	ASN- 335	2.7	152.1	H-Bond (Protein Donor)	false
O4'	O	ASN- 335	2.74	154.41	H-Bond (Ligand Donor)	false
C1'	CG2	VAL- 337	3.86	0	Hydrophobic	false
C5'	CG2	VAL- 337	3.85	0	Hydrophobic	false
C8'	CD1	PHE- 393	3.39	0	Hydrophobic	false
C8'	CE2	PHE- 395	3.72	0	Hydrophobic	false
C6'	CZ	PHE- 417	3.87	0	Hydrophobic	false
O5'	NZ	LYS- 421	3.45	138.92	H-Bond (Protein Donor)	false
O6'	NZ	LYS- 421	3.01	129.82	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 421	3.22	125.62	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 421	3.14	147.51	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 421	3.22	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 421	3.14	0	Ionic (Protein Cationic)	false
O1A	O	HOH- 1386	2.62	159.44	H-Bond (Protein Donor)	false