scPDB - 3n7u entry

Protein Data Bank Entry:

PDB ID : 3n7u

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2010-05-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Formate dehydrogenase, chloroplastic/mitochondrial
ID:	FDH_ARATH
AC:	Q9S7E4
Organism:	Arabidopsis thaliana
Reign:	Eukaryota
TaxID:	3702
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	19.811
Number of residues:	56
Including
Standard Amino Acids:	51
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.118	877.500

% Hydrophobic	% Polar
49.62	50.38
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	68.86 %
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
4.21575	88.2435	121.046

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
C5N	CB	ILE- 122	3.63	0	Hydrophobic	false
C3D	CG2	ILE- 122	4.01	0	Hydrophobic	false
C4N	CG2	VAL- 150	3.25	0	Hydrophobic	false
O2A	N	ARG- 201	2.98	177.08	H-Bond (Protein Donor)	false
O2N	N	ILE- 202	2.84	171.71	H-Bond (Protein Donor)	false
C5D	CD1	ILE- 202	4.26	0	Hydrophobic	false
C5N	CD1	ILE- 202	3.91	0	Hydrophobic	false
O3B	OD2	ASP- 221	2.73	165.23	H-Bond (Ligand Donor)	false
O3B	OD1	ASP- 221	3.39	128.31	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 221	2.67	156.73	H-Bond (Ligand Donor)	false
C1B	CG	MET- 255	4.29	0	Hydrophobic	false
C5B	CG	PRO- 256	4.06	0	Hydrophobic	false
N7N	O	ASN- 282	2.98	165.28	H-Bond (Ligand Donor)	false
N7N	OD2	ASP- 308	3.26	160.65	H-Bond (Ligand Donor)	false
N7N	OD1	ASP- 308	3.4	129.36	H-Bond (Ligand Donor)	false
O7N	NE2	HIS- 332	3.06	144.56	H-Bond (Protein Donor)	false
C2B	CB	GLN- 376	4.2	0	Hydrophobic	false
O2D	O	HOH- 547	2.9	179.97	H-Bond (Protein Donor)	false
O2N	O	HOH- 551	2.78	173.29	H-Bond (Protein Donor)	false
O2B	O	HOH- 553	2.69	159.55	H-Bond (Protein Donor)	false