scPDB - 1u4o entry

Protein Data Bank Entry:

PDB ID : 1u4o

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2004-07-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	L-lactate dehydrogenase
ID:	LDH_PLAFD
AC:	Q27743
Organism:	Plasmodium falciparum
Reign:	Eukaryota
TaxID:	5836
EC Number:	1.1.1.27

Chains:

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

Ligand binding site composition:

B-Factor:	9.758
Number of residues:	21
Including
Standard Amino Acids:	20
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.067	533.250

% Hydrophobic	% Polar
41.14	58.86
According to VolSite

Ligand :

HET Code:	NDD
Formula:	C12H6O4
Molecular weight:	214.174 g/mol
DrugBank ID:	DB08262
Buried Surface Area:	47.47 %
Polar Surface area:	80.26 Å2

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

Mass center Coordinates

X	Y	Z
29.8318	18.7761	5.21462

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
O2'	N	ILE- 31	2.86	160.25	H-Bond (Protein Donor)	false
C1	CB	ILE- 31	3.74	0	Hydrophobic	false
C8	CD1	ILE- 31	3.67	0	Hydrophobic	false
C7	CG1	VAL- 138	3.72	0	Hydrophobic	false
C7	CD2	LEU- 163	4.47	0	Hydrophobic	false
O4'	NE2	HIS- 195	2.64	161.63	H-Bond (Protein Donor)	false
C3	CB	TYR- 247	3.66	0	Hydrophobic	false
C6	CG	PRO- 250	3.81	0	Hydrophobic	false
C7	CB	PRO- 250	3.88	0	Hydrophobic	false
O3'	O	HOH- 668	2.69	179.97	H-Bond (Protein Donor)	false