scPDB - 1wzi entry

Protein Data Bank Entry:

PDB ID : 1wzi

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2005-03-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Malate dehydrogenase
ID:	MDH_THETH
AC:	P10584
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	274
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	14.241
Number of residues:	50
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.589	752.625

% Hydrophobic	% Polar
32.74	67.26
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	55.68 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-10.3775	18.0084	35.9496

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
O1X	N	ALA- 12	2.87	170.89	H-Bond (Protein Donor)	false
O3X	N	ALA- 12	3.31	125.16	H-Bond (Protein Donor)	false
O1A	N	GLN- 14	3.1	167.52	H-Bond (Protein Donor)	false
O1N	NE2	GLN- 14	3	122.62	H-Bond (Protein Donor)	false
O2N	N	ILE- 15	2.62	171.02	H-Bond (Protein Donor)	false
C5N	CD1	ILE- 15	4.01	0	Hydrophobic	false
C5D	CD1	ILE- 15	4.31	0	Hydrophobic	false
O2X	N	SER- 42	2.65	127.48	H-Bond (Protein Donor)	false
O2X	OG	SER- 42	3.28	162.37	H-Bond (Protein Donor)	false
C3N	CG1	VAL- 128	4.13	0	Hydrophobic	false
N7N	O	VAL- 128	3.32	150.91	H-Bond (Ligand Donor)	false
O3D	N	ASN- 130	2.88	150.53	H-Bond (Protein Donor)	false
O2D	ND2	ASN- 130	2.51	148.96	H-Bond (Protein Donor)	false
C2D	CB	ASN- 130	4.06	0	Hydrophobic	false
N7N	O	MET- 154	3.4	159.32	H-Bond (Ligand Donor)	false
C3N	CE	MET- 154	4.1	0	Hydrophobic	false
C4N	CD2	LEU- 157	3.77	0	Hydrophobic	false
C4N	CB	ALA- 245	3.83	0	Hydrophobic	false
O7N	O	HOH- 2358	2.68	180	H-Bond (Protein Donor)	false