scPDB - 1u5a entry

Protein Data Bank Entry:

PDB ID : 1u5a

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2004-07-27

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:	15.240
Number of residues:	23
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.883	438.750

% Hydrophobic	% Polar
49.23	50.77
According to VolSite

Ligand :

HET Code:	BIK
Formula:	C11H7O4
Molecular weight:	203.171 g/mol
DrugBank ID:	DB04641
Buried Surface Area:	42.15 %
Polar Surface area:	80.59 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
23.8113	17.9685	4.77207

Binding mode :

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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
C7	CB	ASN- 140	3.55	0	Hydrophobic	false
O32	CZ	ARG- 171	3.72	0	Ionic (Protein Cationic)	false
O31	CZ	ARG- 171	3.67	0	Ionic (Protein Cationic)	false
O32	NH1	ARG- 171	2.82	170.51	H-Bond (Protein Donor)	false
O31	NH2	ARG- 171	2.92	171.82	H-Bond (Protein Donor)	false
C3	CB	ALA- 236	3.59	0	Hydrophobic	false
O32	O	HOH- 1234	3.23	139.43	H-Bond (Protein Donor)	false