scPDB - 2pk3 entry

Protein Data Bank Entry:

PDB ID : 2pk3

Resolution :1.820 Å

Experimental Method : X-ray

Deposition Date : 2007-04-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	GDP-6-deoxy-D-mannose reductase
ID:	RMD_ANETH
AC:	Q6T1X6
Organism:	Aneurinibacillus thermoaerophilus
Reign:	Bacteria
TaxID:	143495
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	20.884
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.935	462.375

% Hydrophobic	% Polar
41.61	58.39
According to VolSite

Ligand :

HET Code:	A2R
Formula:	C15H20N5O17P3
Molecular weight:	635.264 g/mol
DrugBank ID:	-
Buried Surface Area:	56.77 %
Polar Surface area:	378.8 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	4
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
20.4875	30.0263	23.7565

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
O2	N	PHE- 11	2.94	169.99	H-Bond (Protein Donor)	false
O12	N	VAL- 12	2.92	167.72	H-Bond (Protein Donor)	false
C15'	CG2	VAL- 12	3.99	0	Hydrophobic	false
OP1	NE	ARG- 32	3.46	157.82	H-Bond (Protein Donor)	false
OP2	NH2	ARG- 32	2.65	168.2	H-Bond (Protein Donor)	false
OP2	CZ	ARG- 32	3.59	0	Ionic (Protein Cationic)	false
N6	OD1	ASP- 47	3.1	157.83	H-Bond (Ligand Donor)	false
N1	N	ILE- 48	2.89	171.41	H-Bond (Protein Donor)	false
C15'	CG	LEU- 69	3.96	0	Hydrophobic	false
C1'	CB	ALA- 70	4.44	0	Hydrophobic	false
O4'	N	ALA- 71	3.18	161.76	H-Bond (Protein Donor)	false
C13'	CB	ALA- 71	3.57	0	Hydrophobic	false
O1	OG	SER- 73	2.74	152.87	H-Bond (Protein Donor)	false
O3	OG	SER- 73	3.47	134.54	H-Bond (Protein Donor)	false
C12'	CB	SER- 73	3.78	0	Hydrophobic	false
C14'	CG2	ILE- 112	3.86	0	Hydrophobic	false
C11'	CG2	ILE- 112	3.77	0	Hydrophobic	false
O12'	OH	TYR- 140	2.86	179.69	H-Bond (Protein Donor)	false
O13'	NZ	LYS- 144	2.74	153.06	H-Bond (Protein Donor)	false
O12'	NZ	LYS- 144	3.27	128.4	H-Bond (Protein Donor)	false
O11	NE2	HIS- 170	2.7	168.65	H-Bond (Protein Donor)	false
O1	O	HOH- 543	2.73	179.97	H-Bond (Protein Donor)	false