scPDB - 3i0p entry

Protein Data Bank Entry:

PDB ID : 3i0p

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2009-06-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Malate dehydrogenase, putative
ID:	C4M213_ENTHI
AC:	C4M213
Organism:	Entamoeba histolytica
Reign:	Eukaryota
TaxID:	5759
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.776
Number of residues:	44
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.617	837.000

% Hydrophobic	% Polar
43.15	56.85
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	58.13 %
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
26.8932	28.499	28.2364

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
C5B	CE	MET- 47	4.41	0	Hydrophobic	false
C3D	CE	MET- 47	4.18	0	Hydrophobic	false
C4D	SD	MET- 47	3.8	0	Hydrophobic	false
N7N	O	GLY- 125	2.93	148	H-Bond (Ligand Donor)	false
C3D	CG2	ILE- 126	4.32	0	Hydrophobic	false
O2D	N	ALA- 127	2.89	163.7	H-Bond (Protein Donor)	false
C5N	CB	THR- 163	3.89	0	Hydrophobic	false
C2D	CB	PRO- 165	4.22	0	Hydrophobic	false
C3N	CG	PRO- 165	3.54	0	Hydrophobic	false
O3B	O	CYS- 179	2.84	127.12	H-Bond (Ligand Donor)	false
C4B	CD1	PHE- 180	4.21	0	Hydrophobic	false
O3B	N	ASP- 181	3.05	131.86	H-Bond (Protein Donor)	false
O3D	OD2	ASP- 181	2.5	159.41	H-Bond (Ligand Donor)	false
O3D	OD1	ASP- 181	3.38	126.63	H-Bond (Ligand Donor)	false
O2D	OD1	ASP- 181	2.75	164.76	H-Bond (Ligand Donor)	false
O1N	N	ALA- 183	2.76	163.24	H-Bond (Protein Donor)	false
C5N	CB	ALA- 183	4.16	0	Hydrophobic	false
C5N	CB	PRO- 188	3.94	0	Hydrophobic	false
O2N	CZ	ARG- 191	3.86	0	Ionic (Protein Cationic)	false
O2N	NH2	ARG- 191	2.89	163.35	H-Bond (Protein Donor)	false
O2B	N	GLY- 327	2.69	166.75	H-Bond (Protein Donor)	false
N7A	NZ	LYS- 329	3.27	145.84	H-Bond (Protein Donor)	false
O2B	OE1	GLU- 330	2.68	158.66	H-Bond (Ligand Donor)	false
O3B	O	HOH- 378	3.43	131.17	H-Bond (Ligand Donor)	false
O2B	O	HOH- 410	3.09	179.96	H-Bond (Protein Donor)	false
N7N	O	HOH- 418	3.16	149.11	H-Bond (Ligand Donor)	false