scPDB - 1gz4 entry

Protein Data Bank Entry:

PDB ID : 1gz4

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2002-05-15

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
D	100 %

Ligand binding site composition:

B-Factor:	33.889
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.088	519.750

% Hydrophobic	% Polar
39.61	60.39
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	56.43 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
23.3028	-35.4557	-2.11248

Binding mode :

What is Poseview ?

2D View
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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
O2B	CZ	ARG- 165	3.65	0	Ionic (Protein Cationic)	false
O2A	ND2	ASN- 259	2.88	171.39	H-Bond (Protein Donor)	false
O3'	N	ALA- 312	2.9	154.51	H-Bond (Protein Donor)	false
O2A	N	GLU- 314	2.97	175.06	H-Bond (Protein Donor)	false
O1B	N	ALA- 315	3.09	160.71	H-Bond (Protein Donor)	false
C2'	CB	ASP- 345	4.22	0	Hydrophobic	false
C2'	CD	LYS- 346	3.97	0	Hydrophobic	false
C1'	CB	LYS- 346	4.46	0	Hydrophobic	false
O2'	NZ	LYS- 346	2.83	177.09	H-Bond (Protein Donor)	false
O2'	N	LYS- 346	3.11	170.78	H-Bond (Protein Donor)	false
C1'	CB	ALA- 393	4.23	0	Hydrophobic	false
O3G	OG	SER- 420	2.87	157.15	H-Bond (Protein Donor)	false
O1B	O	HOH- 2135	2.64	179.96	H-Bond (Protein Donor)	false