scPDB - 4gdc entry

Protein Data Bank Entry:

PDB ID : 4gdc

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
A	100 %

Ligand binding site composition:

B-Factor:	42.208
Number of residues:	32
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.160	1059.750

% Hydrophobic	% Polar
49.36	50.64
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	47.99 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
66.3183	71.601	164.577

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
C1B	CD1	ILE- 65	4.39	0	Hydrophobic	false
C4D	CG1	ILE- 65	4.25	0	Hydrophobic	false
C5B	CD2	PHE- 66	3.75	0	Hydrophobic	false
C4B	CG	PHE- 66	3.73	0	Hydrophobic	false
O2A	NE2	HIS- 68	3	151.36	H-Bond (Protein Donor)	false
C1B	CD	ARG- 91	4.05	0	Hydrophobic	false
N1A	OG	SER- 93	3.14	160.15	H-Bond (Protein Donor)	false
O2X	OH	TYR- 104	2.72	140.49	H-Bond (Protein Donor)	false
DuAr	DuAr	TYR- 104	3.93	0	Aromatic Face/Face	false
N6A	OH	TYR- 317	2.98	135.12	H-Bond (Ligand Donor)	false
N7N	OH	TYR- 419	3.4	149.27	H-Bond (Ligand Donor)	false
O7N	NH1	ARG- 447	2.78	145.71	H-Bond (Protein Donor)	false
O7N	NH2	ARG- 447	2.85	141.4	H-Bond (Protein Donor)	false
C4N	CE1	TYR- 453	3.1	0	Hydrophobic	false
O2N	ND2	ASN- 457	3.06	157.84	H-Bond (Protein Donor)	false
O4D	ND2	ASN- 457	3.04	136.23	H-Bond (Protein Donor)	false
N1N	ND2	ASN- 457	3.44	122.92	H-Bond (Protein Donor)	false
C5N	CB	ASN- 457	3.36	0	Hydrophobic	false
O2N	NE2	HIS- 460	3.37	133.17	H-Bond (Protein Donor)	false