scPDB - 2c5e entry

Protein Data Bank Entry:

PDB ID : 2c5e

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2005-10-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	GDP-mannose 3,5-epimerase
ID:	GME_ARATH
AC:	Q93VR3
Organism:	Arabidopsis thaliana
Reign:	Eukaryota
TaxID:	3702
EC Number:	5.1.3.18

Chains:

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

Ligand binding site composition:

B-Factor:	13.694
Number of residues:	50
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:	NAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.520	361.125

% Hydrophobic	% Polar
55.14	44.86
According to VolSite

Ligand :

HET Code:	GDD
Formula:	C16H23N5O16P2
Molecular weight:	603.325 g/mol
DrugBank ID:	-
Buried Surface Area:	83.75 %
Polar Surface area:	352.71 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	8
Rings:	4
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
15.5495	42.4312	8.43331

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
C41	CE	MET- 102	4.1	0	Hydrophobic	false
O21	O	GLY- 103	3	156.02	H-Bond (Ligand Donor)	false
O31	O	GLY- 103	2.94	166.48	H-Bond (Ligand Donor)	false
C3'	CG	MET- 105	4.35	0	Hydrophobic	false
C21	CE	MET- 105	3.93	0	Hydrophobic	false
O1A	N	MET- 105	2.81	176.53	H-Bond (Protein Donor)	false
C31	CG1	ILE- 108	4.37	0	Hydrophobic	false
O41	OG	SER- 143	2.52	146.24	H-Bond (Protein Donor)	false
C61	CB	ALA- 144	4.32	0	Hydrophobic	false
C41	SG	CYS- 145	3.75	0	Hydrophobic	false
O41	OH	TYR- 174	3.42	138.56	H-Bond (Ligand Donor)	false
C41	CE2	TYR- 174	4.2	0	Hydrophobic	false
O2A	ND2	ASN- 203	2.84	147.68	H-Bond (Protein Donor)	false
O2B	ND2	ASN- 203	2.89	131.97	H-Bond (Protein Donor)	false
O6A	N	ASN- 203	2.74	151.18	H-Bond (Protein Donor)	false
C61	CB	ASN- 203	4.4	0	Hydrophobic	false
N2	O	GLU- 216	3.19	145.29	H-Bond (Ligand Donor)	false
C1'	CB	ALA- 218	4.48	0	Hydrophobic	false
C5'	CB	ALA- 218	3.8	0	Hydrophobic	false
O2A	N	ALA- 218	2.81	157.66	H-Bond (Protein Donor)	false
O6	NZ	LYS- 225	2.69	171.72	H-Bond (Protein Donor)	false
N7	N	TRP- 236	3.06	155.71	H-Bond (Protein Donor)	false
C2'	CE3	TRP- 236	4.22	0	Hydrophobic	false
O3'	NE2	GLN- 241	3.03	157.44	H-Bond (Protein Donor)	false
C5'	CG	ARG- 243	4.19	0	Hydrophobic	false
O2B	NE	ARG- 243	2.94	150.22	H-Bond (Protein Donor)	false
O3B	NE	ARG- 243	3.12	139.23	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 243	2.82	152.89	H-Bond (Protein Donor)	false
O3B	CZ	ARG- 243	3.4	0	Ionic (Protein Cationic)	false
C1'	CG	MET- 277	4.27	0	Hydrophobic	false
C4'	SD	MET- 277	3.82	0	Hydrophobic	false
O2'	O	PRO- 300	2.79	165.43	H-Bond (Ligand Donor)	false
O3'	O	GLU- 301	2.67	154.53	H-Bond (Ligand Donor)	false
O6	OG	SER- 356	2.6	135.93	H-Bond (Protein Donor)	false
C61	C4N	NAD- 1381	3.56	0	Hydrophobic	false