scPDB - 4ajp entry

Protein Data Bank Entry:

PDB ID : 4ajp

Resolution :2.380 Å

Experimental Method : X-ray

Deposition Date : 2012-02-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	7.030	7.030	7.030	0.000	7.030	1

List of CHEMBLId :

CHEMBL2059811

Binding Site :

Uniprot Annotation

Name:	L-lactate dehydrogenase A chain
ID:	LDHA_HUMAN
AC:	P00338
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.1.1.27

Chains:

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

Ligand binding site composition:

B-Factor:	34.132
Number of residues:	48
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.204	675.000

% Hydrophobic	% Polar
54.00	46.00
According to VolSite

Ligand :

HET Code:	88N
Formula:	C25H25N3O6S
Molecular weight:	495.547 g/mol
DrugBank ID:	-
Buried Surface Area:	62.82 %
Polar Surface area:	179.59 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
2.21703	-43.1092	26.4916

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
C5	CG1	VAL- 25	4.2	0	Hydrophobic	false
C20	CG2	VAL- 30	4.09	0	Hydrophobic	false
C27	CG2	VAL- 30	3.5	0	Hydrophobic	false
C6	CB	ASP- 51	4.37	0	Hydrophobic	false
N11	OD2	ASP- 51	3.06	166.95	H-Bond (Ligand Donor)	false
C5	CG1	VAL- 52	4.17	0	Hydrophobic	false
C1	CG1	VAL- 52	4.49	0	Hydrophobic	false
S10	CG1	VAL- 52	4.29	0	Hydrophobic	false
C9	CG2	VAL- 52	3.86	0	Hydrophobic	false
C6	CB	ALA- 95	3.47	0	Hydrophobic	false
C8	CB	ALA- 95	3.97	0	Hydrophobic	false
N16	O	GLY- 96	2.85	136.01	H-Bond (Ligand Donor)	false
O13	N	GLY- 96	2.77	174.19	H-Bond (Protein Donor)	false
C27	CB	ARG- 98	4.5	0	Hydrophobic	false
C21	CB	ARG- 98	4.5	0	Hydrophobic	false
C20	CD	ARG- 98	4.46	0	Hydrophobic	false
O31	NE2	GLN- 99	2.73	161.84	H-Bond (Protein Donor)	false
O31	NE	ARG- 105	3.18	122.02	H-Bond (Protein Donor)	false
O32	NE	ARG- 105	2.85	178.05	H-Bond (Protein Donor)	false
O35	NH2	ARG- 105	3.04	155.43	H-Bond (Protein Donor)	false
O31	CZ	ARG- 105	3.64	0	Ionic (Protein Cationic)	false
O32	CZ	ARG- 105	3.63	0	Ionic (Protein Cationic)	false
C1	CG2	ILE- 115	4.43	0	Hydrophobic	false
S10	CG2	ILE- 115	3.94	0	Hydrophobic	false
C1	CD2	PHE- 118	3.51	0	Hydrophobic	false
C5	CD1	ILE- 119	4.28	0	Hydrophobic	false
C24	CG1	VAL- 135	4.06	0	Hydrophobic	false
O32	ND2	ASN- 137	2.71	145.84	H-Bond (Protein Donor)	false
O34	NH1	ARG- 168	3.49	127.33	H-Bond (Protein Donor)	false
O34	NH2	ARG- 168	2.74	161.94	H-Bond (Protein Donor)	false
O35	NH1	ARG- 168	3.02	172.99	H-Bond (Protein Donor)	false
O34	CZ	ARG- 168	3.55	0	Ionic (Protein Cationic)	false
O35	CZ	ARG- 168	3.86	0	Ionic (Protein Cationic)	false
O32	NE2	HIS- 192	2.64	154.29	H-Bond (Protein Donor)	false
C29	CB	ALA- 237	4.11	0	Hydrophobic	false
C29	CG2	THR- 247	4.47	0	Hydrophobic	false
O34	OG1	THR- 247	2.8	173.28	H-Bond (Protein Donor)	false
C28	CB	ILE- 251	3.94	0	Hydrophobic	false
C24	CG1	ILE- 251	4.26	0	Hydrophobic	false