scPDB - 1pjl entry

Protein Data Bank Entry:

PDB ID : 1pjl

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2003-06-03

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
E	12 %
H	88 %

Ligand binding site composition:

B-Factor:	38.522
Number of residues:	24
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.432	2052.000

% Hydrophobic	% Polar
31.74	68.26
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	37.43 %
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
-7.66545	57.5944	-23.9353

Binding mode :

What is Poseview ?

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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
C1B	CD	LYS- 7156	4.45	0	Hydrophobic	false
N1A	N	ARG- 7194	2.79	152.45	H-Bond (Protein Donor)	false
C1B	CG2	ILE- 7479	3.99	0	Hydrophobic	false
C1B	CD2	LEU- 7480	4.42	0	Hydrophobic	false
O2A	CZ	ARG- 7542	3.35	0	Ionic (Protein Cationic)	false
C5B	CG	ARG- 7542	4	0	Hydrophobic	false
O2A	OH	TYR- 7552	2.9	168.56	H-Bond (Protein Donor)	false
O5B	OH	TYR- 7552	3.36	126.29	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 7556	3.06	0	Ionic (Protein Cationic)	false
O3	NE	ARG- 7556	3.35	172.06	H-Bond (Protein Donor)	false