scPDB - 4wlo entry

Protein Data Bank Entry:

PDB ID : 4wlo

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2014-10-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Malate dehydrogenase, mitochondrial
ID:	MDHM_HUMAN
AC:	P40926
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.1.1.37

Chains:

Chain Name:	Percentage of Residues within binding site
B	2 %
C	98 %

Ligand binding site composition:

B-Factor:	47.338
Number of residues:	46
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.461	1032.750

% Hydrophobic	% Polar
53.92	46.08
According to VolSite

Ligand :

HET Code:	NAI
Formula:	C21H27N7O14P2
Molecular weight:	663.425 g/mol
DrugBank ID:	DB00157
Buried Surface Area:	64.35 %
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
35.1224	-15.1034	-39.205

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
O2A	N	GLY- 35	2.82	155.96	H-Bond (Protein Donor)	false
O2N	N	ILE- 36	2.88	165.31	H-Bond (Protein Donor)	false
C1D	CD1	ILE- 36	3.95	0	Hydrophobic	false
C5D	CD1	ILE- 36	3.99	0	Hydrophobic	false
O2B	OD1	ASP- 57	2.66	154.62	H-Bond (Ligand Donor)	false
O4B	N	GLY- 101	3.37	151.6	H-Bond (Protein Donor)	false
C2D	CB	PRO- 103	4.43	0	Hydrophobic	false
C1D	CG2	ILE- 140	4.48	0	Hydrophobic	false
N7N	O	ILE- 140	3.16	149.73	H-Bond (Ligand Donor)	false
C4N	CD2	LEU- 172	4.29	0	Hydrophobic	false
C4N	SD	MET- 251	3.46	0	Hydrophobic	false