scPDB - 5mdh entry

Protein Data Bank Entry:

PDB ID : 5mdh

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 1998-10-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Malate dehydrogenase, cytoplasmic
ID:	MDHC_PIG
AC:	P11708
Organism:	Sus scrofa
Reign:	Eukaryota
TaxID:	9823
EC Number:	1.1.1.37

Chains:

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

Ligand binding site composition:

B-Factor:	37.809
Number of residues:	48
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.030	732.375

% Hydrophobic	% Polar
47.00	53.00
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	65.63 %
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
33.6284	21.6572	16.5866

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
N3A	N	GLY- 10	3.41	121.23	H-Bond (Protein Donor)	false
O1A	N	GLN- 14	3.22	174.49	H-Bond (Protein Donor)	false
O2N	N	ILE- 15	3.4	163.14	H-Bond (Protein Donor)	false
C2D	CD1	ILE- 15	4.44	0	Hydrophobic	false
C5N	CD1	ILE- 15	4.04	0	Hydrophobic	false
C5D	CD1	ILE- 15	3.45	0	Hydrophobic	false
O3B	OD2	ASP- 41	2.56	151.96	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 41	3.46	131.3	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 41	2.75	173.85	H-Bond (Ligand Donor)	false
C5D	CG1	VAL- 86	3.58	0	Hydrophobic	false
O4B	N	SER- 88	3.48	154	H-Bond (Protein Donor)	false
C4D	CB	SER- 88	3.69	0	Hydrophobic	false
C3D	CB	PRO- 90	3.98	0	Hydrophobic	false
N7N	O	VAL- 128	3.3	173.61	H-Bond (Ligand Donor)	false
C3N	CG1	VAL- 128	3.44	0	Hydrophobic	false
O3D	N	ASN- 130	3.29	176.49	H-Bond (Protein Donor)	false
C3N	CD2	LEU- 154	4.49	0	Hydrophobic	false
N7N	O	LEU- 154	3.49	171.71	H-Bond (Ligand Donor)	false
C4N	CD2	LEU- 157	3.94	0	Hydrophobic	false
O1N	OG	SER- 240	2.82	147.35	H-Bond (Protein Donor)	false
C5N	CB	ALA- 245	3.61	0	Hydrophobic	false
O2N	O	HOH- 355	3.17	152.74	H-Bond (Protein Donor)	false
O7N	O	HOH- 378	3.18	179.95	H-Bond (Protein Donor)	false