scPDB - 2d1c entry

Protein Data Bank Entry:

PDB ID : 2d1c

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2005-08-15

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:	IDH_THET8
AC:	P33197
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	1.1.1.42

Chains:

Chain Name:	Percentage of Residues within binding site
A	77 %
B	23 %

Ligand binding site composition:

B-Factor:	23.372
Number of residues:	58
Including
Standard Amino Acids:	52
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.014	1272.375

% Hydrophobic	% Polar
34.22	65.78
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	66.22 %
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
22.5539	60.3485	56.6617

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	NZ	LYS- 85	3.47	123.98	H-Bond (Protein Donor)	false
C3N	CB	PRO- 87	4.49	0	Hydrophobic	false
O7N	N	LEU- 88	2.89	161.47	H-Bond (Protein Donor)	false
C3D	CG	GLU- 89	4.46	0	Hydrophobic	false
O3D	O	THR- 90	2.6	141.55	H-Bond (Ligand Donor)	false
O3D	N	THR- 90	2.64	144.99	H-Bond (Protein Donor)	false
O2D	ND2	ASN- 193	2.96	157.12	H-Bond (Protein Donor)	false
C2D	CD1	ILE- 222	4.15	0	Hydrophobic	false
C5B	CB	ASN- 225	4.17	0	Hydrophobic	false
O2B	NE2	GLN- 229	3.46	132.97	H-Bond (Protein Donor)	false
O2X	NE2	GLN- 229	3.14	151.96	H-Bond (Protein Donor)	false
O2X	NZ	LYS- 232	3.18	159.19	H-Bond (Protein Donor)	false
O2X	NZ	LYS- 232	3.18	0	Ionic (Protein Cationic)	false
C1B	CB	LEU- 261	4.37	0	Hydrophobic	false
C5B	CD1	LEU- 261	4.23	0	Hydrophobic	false
N7N	OE1	GLU- 277	3.15	165.63	H-Bond (Ligand Donor)	false
N6A	NE2	HIS- 280	3.26	139.39	H-Bond (Ligand Donor)	false
O1A	N	GLY- 281	2.77	165.68	H-Bond (Protein Donor)	false
C4D	CB	SER- 282	4.15	0	Hydrophobic	false
O4D	N	SER- 282	3.15	165.78	H-Bond (Protein Donor)	false
O1X	NZ	LYS- 285	2.81	142.82	H-Bond (Protein Donor)	false
O1X	NZ	LYS- 285	2.81	0	Ionic (Protein Cationic)	false
O3X	OH	TYR- 286	2.7	154.32	H-Bond (Protein Donor)	false
C2B	CE2	TYR- 286	4.01	0	Hydrophobic	false
N6A	O	ASN- 293	2.83	157.39	H-Bond (Ligand Donor)	false
N1A	N	ASN- 293	3.27	140.14	H-Bond (Protein Donor)	false
O2N	O	HOH- 1618	2.69	175.42	H-Bond (Protein Donor)	false
O2X	O	HOH- 1975	2.91	138.27	H-Bond (Protein Donor)	false