scPDB - 4ajj entry

Protein Data Bank Entry:

PDB ID : 4ajj

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2012-02-16

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	97 %
D	3 %

Ligand binding site composition:

B-Factor:	17.812
Number of residues:	39
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.380	378.000

% Hydrophobic	% Polar
45.54	54.46
According to VolSite

Ligand :

HET Code:	88R
Formula:	C12H12O6
Molecular weight:	252.220 g/mol
DrugBank ID:	-
Buried Surface Area:	70.36 %
Polar Surface area:	98.72 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	0
Rings:	1
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
26.2635	15.6965	49.3134

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
C10	CG2	VAL- 30	3.33	0	Hydrophobic	false
C7	CG2	VAL- 30	3.45	0	Hydrophobic	false
C8	CG2	VAL- 30	3.21	0	Hydrophobic	false
C1	CB	THR- 94	4.41	0	Hydrophobic	false
C10	CG	ARG- 98	4.36	0	Hydrophobic	false
O15	NE2	GLN- 99	2.68	156.87	H-Bond (Protein Donor)	false
O14	NE	ARG- 105	2.89	165.79	H-Bond (Protein Donor)	false
O14	NH2	ARG- 105	3.31	136.35	H-Bond (Protein Donor)	false
O17	NH2	ARG- 105	3.17	147.98	H-Bond (Protein Donor)	false
O14	CZ	ARG- 105	3.54	0	Ionic (Protein Cationic)	false
O15	CZ	ARG- 105	3.88	0	Ionic (Protein Cationic)	false
C4	CG1	VAL- 135	3.92	0	Hydrophobic	false
C1	CB	SER- 136	4.27	0	Hydrophobic	false
O14	ND2	ASN- 137	2.68	133.23	H-Bond (Protein Donor)	false
C11	CD2	LEU- 164	4.46	0	Hydrophobic	false
O17	CZ	ARG- 168	3.77	0	Ionic (Protein Cationic)	false
O18	CZ	ARG- 168	3.5	0	Ionic (Protein Cationic)	false
O17	NH1	ARG- 168	2.97	171.13	H-Bond (Protein Donor)	false
O18	NH2	ARG- 168	2.63	159.87	H-Bond (Protein Donor)	false
O14	NE2	HIS- 192	2.64	154.81	H-Bond (Protein Donor)	false
C12	CB	ALA- 237	4.18	0	Hydrophobic	false
C10	CB	TYR- 246	4.27	0	Hydrophobic	false
C12	CG2	THR- 247	4.47	0	Hydrophobic	false
O18	OG1	THR- 247	2.65	171.79	H-Bond (Protein Donor)	false
C11	CB	ILE- 251	3.87	0	Hydrophobic	false
C5	CG1	ILE- 251	4.16	0	Hydrophobic	false