scPDB - 2jkv entry

Protein Data Bank Entry:

PDB ID : 2jkv

Resolution :2.530 Å

Experimental Method : X-ray

Deposition Date : 2008-09-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	6-phosphogluconate dehydrogenase, decarboxylating
ID:	6PGD_HUMAN
AC:	P52209
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.1.1.44

Chains:

Chain Name:	Percentage of Residues within binding site
A	79 %
B	21 %

Ligand binding site composition:

B-Factor:	30.031
Number of residues:	51
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	CL

Cavity properties

Ligandability	Volume (Å3)
0.654	941.625

% Hydrophobic	% Polar
42.65	57.35
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	64.26 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
35.7518	21.1508	-28.5152

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
O3B	N	LEU- 11	3.3	133.67	H-Bond (Protein Donor)	false
C5B	CB	ALA- 12	3.91	0	Hydrophobic	false
O2N	N	MET- 14	2.91	156.65	H-Bond (Protein Donor)	false
C5D	CB	MET- 14	4.14	0	Hydrophobic	false
C3N	CG	MET- 14	3.69	0	Hydrophobic	false
C5N	CE	MET- 14	3.49	0	Hydrophobic	false
O3B	OD1	ASN- 33	2.79	132.23	H-Bond (Ligand Donor)	false
O1X	ND2	ASN- 33	3.31	123.52	H-Bond (Protein Donor)	false
O3X	ND2	ASN- 33	2.87	173.24	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 34	3.78	0	Ionic (Protein Cationic)	false
O2X	CZ	ARG- 34	3.97	0	Ionic (Protein Cationic)	false
O1X	NE	ARG- 34	3.07	170.45	H-Bond (Protein Donor)	false
O2X	NH2	ARG- 34	2.98	159.19	H-Bond (Protein Donor)	false
O1X	N	THR- 35	2.97	141.26	H-Bond (Protein Donor)	false
O2X	NZ	LYS- 38	3.59	0	Ionic (Protein Cationic)	false
O3X	NZ	LYS- 38	2.58	0	Ionic (Protein Cationic)	false
O3X	NZ	LYS- 38	2.58	162.28	H-Bond (Protein Donor)	false
C4D	CD2	LEU- 74	3.96	0	Hydrophobic	false
C4B	CB	VAL- 75	4.3	0	Hydrophobic	false
C1B	CB	VAL- 75	3.75	0	Hydrophobic	false
O3D	O	VAL- 75	2.64	161	H-Bond (Ligand Donor)	false
O4B	N	LYS- 76	3.11	164.66	H-Bond (Protein Donor)	false
O3D	N	ASN- 103	3.18	150.61	H-Bond (Protein Donor)	false
O2D	N	ASN- 103	3.49	145.2	H-Bond (Protein Donor)	false
C2D	CB	ASN- 103	4.36	0	Hydrophobic	false
N7N	O	GLY- 451	3.36	147.88	H-Bond (Ligand Donor)	false
O1A	OG	SER- 478	3.1	145.6	H-Bond (Protein Donor)	false
O1A	N	SER- 479	3.27	168.42	H-Bond (Protein Donor)	false
O2A	OH	TYR- 481	2.75	173.28	H-Bond (Protein Donor)	false
O2D	O	HOH- 2039	3.04	168.26	H-Bond (Ligand Donor)	false
O2N	O	HOH- 2263	2.83	175.97	H-Bond (Protein Donor)	false