scPDB - 4al4 entry

Protein Data Bank Entry:

PDB ID : 4al4

Resolution :1.780 Å

Experimental Method : X-ray

Deposition Date : 2012-03-01

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_RAT
AC:	P04642
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	1.1.1.27

Chains:

Chain Name:	Percentage of Residues within binding site
C	98 %
D	2 %

Ligand binding site composition:

B-Factor:	23.639
Number of residues:	22
Including
Standard Amino Acids:	19
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.095	681.750

% Hydrophobic	% Polar
51.49	48.51
According to VolSite

Ligand :

HET Code:	W7E
Formula:	C24H24N4O7S
Molecular weight:	512.535 g/mol
DrugBank ID:	-
Buried Surface Area:	62.39 %
Polar Surface area:	200.85 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	3
Rings:	3
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
31.5376	12.0108	50.3737

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
O33	N	ALA- 29	2.83	157.64	H-Bond (Protein Donor)	false
C1	CG1	VAL- 52	3.86	0	Hydrophobic	false
S10	CG2	VAL- 52	4.43	0	Hydrophobic	false
C15	CB	ALA- 97	4.46	0	Hydrophobic	false
C28	CG	ARG- 98	3.61	0	Hydrophobic	false
C23	CB	ARG- 98	4.01	0	Hydrophobic	false
C27	CD	ARG- 98	3.65	0	Hydrophobic	false
O32	CZ	ARG- 98	3.72	0	Ionic (Protein Cationic)	false
O22	N	ARG- 98	3.25	159.81	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 98	3.63	162.82	Pi/Cation	false
C14	CG	ARG- 111	3.86	0	Hydrophobic	false
C15	CD	ARG- 111	3.53	0	Hydrophobic	false
O18	NH1	ARG- 111	3.07	157.09	H-Bond (Protein Donor)	false
C14	CD1	ILE- 115	4.08	0	Hydrophobic	false
C6	CG1	ILE- 115	3.49	0	Hydrophobic	false