scPDB - 4i9n entry

Protein Data Bank Entry:

PDB ID : 4i9n

Resolution :2.350 Å

Experimental Method : X-ray

Deposition Date : 2012-12-05

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 A chain
ID:	LDHA_RABIT
AC:	P13491
Organism:	Oryctolagus cuniculus
Reign:	Eukaryota
TaxID:	9986
EC Number:	1.1.1.27

Chains:

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

Ligand binding site composition:

B-Factor:	35.493
Number of residues:	27
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.617	394.875

% Hydrophobic	% Polar
56.41	43.59
According to VolSite

Ligand :

HET Code:	1E6
Formula:	C18H18ClN2O7S
Molecular weight:	441.863 g/mol
DrugBank ID:	-
Buried Surface Area:	50.25 %
Polar Surface area:	166.34 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	3
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
47.075	5.98297	119.916

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
CL3	CG1	VAL- 25	4.3	0	Hydrophobic	false
O28	OD2	ASP- 51	3.27	141.05	H-Bond (Ligand Donor)	false
CL3	CB	ASP- 51	4.37	0	Hydrophobic	false
C11	CG1	VAL- 52	4.23	0	Hydrophobic	false
C17	CG1	VAL- 52	3.78	0	Hydrophobic	false
C18	CG2	VAL- 52	4.45	0	Hydrophobic	false
C21	CG2	VAL- 52	4.32	0	Hydrophobic	false
CL3	CB	ALA- 95	3.76	0	Hydrophobic	false
C18	CB	ALA- 95	3.69	0	Hydrophobic	false
O4	NE	ARG- 111	3.46	152.24	H-Bond (Protein Donor)	false
C9	CB	ASN- 114	4.01	0	Hydrophobic	false
C17	CG2	ILE- 115	4.4	0	Hydrophobic	false
C21	CG2	ILE- 115	4.15	0	Hydrophobic	false
C38	CD1	ILE- 115	4.1	0	Hydrophobic	false
C9	CG1	ILE- 115	3.46	0	Hydrophobic	false
S10	CB	PHE- 118	3.6	0	Hydrophobic	false
C11	CD2	PHE- 118	3.45	0	Hydrophobic	false
C17	CD1	ILE- 119	4.14	0	Hydrophobic	false