scPDB - 4gdd entry

Protein Data Bank Entry:

PDB ID : 4gdd

Resolution :2.750 Å

Experimental Method : X-ray

Deposition Date : 2012-07-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-galactopyranose mutase
ID:	Q4W1X2_ASPFM
AC:	Q4W1X2
Organism:	Neosartorya fumigata
Reign:	Eukaryota
TaxID:	746128
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	44.835
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.082	1049.625

% Hydrophobic	% Polar
45.98	54.02
According to VolSite

Ligand :

HET Code:	NAI
Formula:	C21H27N7O14P2
Molecular weight:	663.425 g/mol
DrugBank ID:	DB00157
Buried Surface Area:	52.32 %
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
22.5687	95.4748	205.705

Binding mode :

What is Poseview ?

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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	CD1	ILE- 65	4.33	0	Hydrophobic	false
C4D	CG1	ILE- 65	4.19	0	Hydrophobic	false
C5B	CG	PHE- 66	3.65	0	Hydrophobic	false
C4B	CD1	PHE- 66	3.74	0	Hydrophobic	false
O1A	NE2	HIS- 68	2.89	165.33	H-Bond (Protein Donor)	false
C1B	CD	ARG- 91	3.87	0	Hydrophobic	false
N1A	OG	SER- 93	2.91	175.33	H-Bond (Protein Donor)	false
O2B	OH	TYR- 104	3.32	172.67	H-Bond (Ligand Donor)	false
DuAr	DuAr	TYR- 104	3.78	0	Aromatic Face/Face	false
N7N	OH	TYR- 419	3.13	133.19	H-Bond (Ligand Donor)	false
O7N	NH1	ARG- 447	2.63	149.27	H-Bond (Protein Donor)	false
O7N	NH2	ARG- 447	3.06	129.46	H-Bond (Protein Donor)	false
C4N	CD1	TYR- 453	3.62	0	Hydrophobic	false
O1N	ND2	ASN- 457	3.12	151.03	H-Bond (Protein Donor)	false
O4D	ND2	ASN- 457	3.24	135.56	H-Bond (Protein Donor)	false
C4N	CB	ASN- 457	4.01	0	Hydrophobic	false