scPDB - 1v9n entry

Protein Data Bank Entry:

PDB ID : 1v9n

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2004-01-26

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_PYRHO
AC:	O59028
Organism:	Pyrococcus horikoshii
Reign:	Archaea
TaxID:	70601
EC Number:	1.1.1.37

Chains:

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

Ligand binding site composition:

B-Factor:	27.061
Number of residues:	46
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.249	783.000

% Hydrophobic	% Polar
37.07	62.93
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	61.68 %
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
17.4202	67.1249	94.4046

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
O2X	NZ	LYS- 4	3.98	0	Ionic (Protein Cationic)	false
O3X	NZ	LYS- 4	2.85	0	Ionic (Protein Cationic)	false
O3X	NZ	LYS- 4	2.85	139.49	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 50	3.91	0	Ionic (Protein Cationic)	false
O2X	NH2	ARG- 50	3.09	167.46	H-Bond (Protein Donor)	false
C4D	CG1	VAL- 52	3.68	0	Hydrophobic	false
N7N	O	GLY- 129	2.98	154.84	H-Bond (Ligand Donor)	false
C3D	CG2	ILE- 130	4.38	0	Hydrophobic	false
O2D	N	ALA- 131	3.13	158.19	H-Bond (Protein Donor)	false
C5N	CB	THR- 167	3.74	0	Hydrophobic	false
C2D	CB	PRO- 169	3.94	0	Hydrophobic	false
C3N	CG	PRO- 169	3.81	0	Hydrophobic	false
C4B	CD1	LEU- 183	4.15	0	Hydrophobic	false
O3B	N	ASP- 184	2.89	142.46	H-Bond (Protein Donor)	false
O2D	OD2	ASP- 184	3.17	141.1	H-Bond (Ligand Donor)	false
C5B	CB	MET- 185	3.91	0	Hydrophobic	false
O1N	N	ALA- 186	2.8	174.98	H-Bond (Protein Donor)	false
C5N	CB	ALA- 186	3.93	0	Hydrophobic	false
C5D	CG	PRO- 191	3.31	0	Hydrophobic	false
C5N	CB	PRO- 191	4.37	0	Hydrophobic	false
O4B	ND1	HIS- 322	3.23	135.01	H-Bond (Protein Donor)	false
C1B	CB	HIS- 322	4.23	0	Hydrophobic	false
O2B	N	GLY- 323	3.1	141.96	H-Bond (Protein Donor)	false
N7A	NZ	LYS- 325	3.15	145.5	H-Bond (Protein Donor)	false
O1X	N	GLY- 326	2.82	166.96	H-Bond (Protein Donor)	false
N7N	O	HOH- 410	3.05	143.46	H-Bond (Ligand Donor)	false