scPDB - 2d4v entry

Protein Data Bank Entry:

PDB ID : 2d4v

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2005-10-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Isocitrate dehydrogenase [NADP]
ID:	Q8GAX0_ACITH
AC:	Q8GAX0
Organism:	Acidithiobacillus thiooxidans
Reign:	Bacteria
TaxID:	930
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	24 %
D	76 %

Ligand binding site composition:

B-Factor:	7.800
Number of residues:	56
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.556	972.000

% Hydrophobic	% Polar
37.50	62.50
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	64.56 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
18.0356	102.344	51.1197

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
O7N	N	LEU- 103	2.77	162.88	H-Bond (Protein Donor)	false
O3D	N	THR- 105	3.01	146.57	H-Bond (Protein Donor)	false
O2D	N	THR- 105	3.43	136.64	H-Bond (Protein Donor)	false
O3D	O	THR- 105	2.81	139.07	H-Bond (Ligand Donor)	false
O2D	ND2	ASN- 232	2.96	155.81	H-Bond (Protein Donor)	false
C3D	CD1	ILE- 294	4.34	0	Hydrophobic	false
C5B	CB	ASN- 297	4.11	0	Hydrophobic	false
C5B	CD1	ILE- 333	4.34	0	Hydrophobic	false
N7N	OE1	GLU- 349	2.83	171.66	H-Bond (Ligand Donor)	false
N6A	NE2	HIS- 352	3.43	146.51	H-Bond (Ligand Donor)	false
O2A	N	GLY- 353	2.78	154.95	H-Bond (Protein Donor)	false
C4D	CB	THR- 354	4.41	0	Hydrophobic	false
O4D	N	THR- 354	3.16	163.09	H-Bond (Protein Donor)	false
O1A	N	ALA- 355	2.64	150.31	H-Bond (Protein Donor)	false
C2B	CB	ALA- 355	3.62	0	Hydrophobic	false
C5D	CG	PRO- 356	4.46	0	Hydrophobic	false
O3B	OD2	ASP- 357	2.62	165.18	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 357	2.67	168.45	H-Bond (Ligand Donor)	false
N6A	O	ASN- 365	2.94	161.62	H-Bond (Ligand Donor)	false
N1A	N	ASN- 365	2.83	165.74	H-Bond (Protein Donor)	false
O1N	O	HOH- 3307	2.73	179.96	H-Bond (Protein Donor)	false