scPDB - 1pj2 entry

Protein Data Bank Entry:

PDB ID : 1pj2

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2003-05-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD-dependent malic enzyme, mitochondrial
ID:	MAOM_HUMAN
AC:	P23368
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.1.1.38

Chains:

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

Ligand binding site composition:

B-Factor:	28.974
Number of residues:	59
Including
Standard Amino Acids:	54
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.486	675.000

% Hydrophobic	% Polar
39.00	61.00
According to VolSite

Ligand :

HET Code:	NAI
Formula:	C21H27N7O14P2
Molecular weight:	663.425 g/mol
DrugBank ID:	DB00157
Buried Surface Area:	69.38 %
Polar Surface area:	342.9 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	6
Rings:	5
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
87.7791	-7.8523	1.0725

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
O1N	NH1	ARG- 165	2.72	151.04	H-Bond (Protein Donor)	false
O1N	CZ	ARG- 165	3.69	0	Ionic (Protein Cationic)	false
O2A	ND2	ASN- 259	2.8	155.24	H-Bond (Protein Donor)	false
C4N	CG2	THR- 283	3.46	0	Hydrophobic	false
O3B	N	ALA- 312	3	159	H-Bond (Protein Donor)	false
O2A	N	GLU- 314	3.03	166.07	H-Bond (Protein Donor)	false
O2N	N	ALA- 315	3	153.19	H-Bond (Protein Donor)	false
C2B	CB	ASP- 345	4.2	0	Hydrophobic	false
O2B	N	LYS- 346	3.35	165.72	H-Bond (Protein Donor)	false
C1B	CB	ALA- 393	4.11	0	Hydrophobic	false
N7N	O	LEU- 419	2.97	159.07	H-Bond (Ligand Donor)	false
C4D	CB	SER- 420	4.25	0	Hydrophobic	false
C1D	CB	SER- 420	4.5	0	Hydrophobic	false
O3D	N	ASN- 421	3.48	144.5	H-Bond (Protein Donor)	false
O2D	N	ASN- 421	3.25	145.07	H-Bond (Protein Donor)	false
O3D	O	ASN- 421	3.27	148.44	H-Bond (Ligand Donor)	false
N7N	O	GLY- 465	3.09	142.9	H-Bond (Ligand Donor)	false
O7N	N	ASN- 467	3.03	135.27	H-Bond (Protein Donor)	false
O2N	O	HOH- 4007	2.68	179.95	H-Bond (Protein Donor)	false