scPDB - 4i9h entry

Protein Data Bank Entry:

PDB ID : 4i9h

Resolution :2.170 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	2 %
H	98 %

Ligand binding site composition:

B-Factor:	35.850
Number of residues:	50
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.946	610.875

% Hydrophobic	% Polar
45.30	54.70
According to VolSite

Ligand :

HET Code:	1E4
Formula:	C33H29ClFN3O12S
Molecular weight:	746.113 g/mol
DrugBank ID:	-
Buried Surface Area:	52.43 %
Polar Surface area:	269.04 Å2

Number of
H-Bond Acceptors:	15
H-Bond Donors:	5
Rings:	4
Aromatic rings:	4
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	17

Mass center Coordinates

X	Y	Z
54.8725	33.2644	104.633

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
CL4	CG1	VAL- 25	3.61	0	Hydrophobic	false
C16	CG2	VAL- 30	4.4	0	Hydrophobic	false
C23	CG1	VAL- 30	3.88	0	Hydrophobic	false
C21	CG2	VAL- 30	3.42	0	Hydrophobic	false
CL4	CB	ASP- 51	4.2	0	Hydrophobic	false
O71	OD2	ASP- 51	3.35	140.67	H-Bond (Ligand Donor)	false
C6	CG1	VAL- 52	3.97	0	Hydrophobic	false
C43	CG2	VAL- 52	4.01	0	Hydrophobic	false
C49	CG1	VAL- 52	3.84	0	Hydrophobic	false
C2	CG2	VAL- 52	4.05	0	Hydrophobic	false
F30	CB	THR- 94	3.39	0	Hydrophobic	false
C10	CB	ALA- 95	3.8	0	Hydrophobic	false
CL4	CB	ALA- 95	3.52	0	Hydrophobic	false
C5	CB	ALA- 95	3.44	0	Hydrophobic	false
O75	O	GLY- 96	2.99	162.32	H-Bond (Ligand Donor)	false
O64	NH1	ARG- 111	3.5	143.78	H-Bond (Protein Donor)	false
C56	CB	ASN- 114	3.86	0	Hydrophobic	false
C2	CD1	ILE- 115	3.91	0	Hydrophobic	false
C6	CG2	ILE- 115	4.23	0	Hydrophobic	false
C57	CG1	ILE- 115	3.55	0	Hydrophobic	false
C49	CD2	PHE- 118	4.04	0	Hydrophobic	false
S51	CB	PHE- 118	3.62	0	Hydrophobic	false
C6	CD1	ILE- 119	3.71	0	Hydrophobic	false
F30	CB	VAL- 135	3.33	0	Hydrophobic	false
C23	CG1	VAL- 135	3.79	0	Hydrophobic	false
F30	CB	SER- 136	4.05	0	Hydrophobic	false
O65	CZ	ARG- 168	3.89	0	Ionic (Protein Cationic)	false
O67	CZ	ARG- 168	3.57	0	Ionic (Protein Cationic)	false
O65	NH2	ARG- 168	2.99	164.1	H-Bond (Protein Donor)	false
O67	NH1	ARG- 168	2.84	161.47	H-Bond (Protein Donor)	false
O67	NH2	ARG- 168	3.43	131.48	H-Bond (Protein Donor)	false
O67	OG1	THR- 247	2.79	166.07	H-Bond (Protein Donor)	false
C32	CD1	ILE- 251	4.22	0	Hydrophobic	false
N35	O	HOH- 534	2.94	179.98	H-Bond (Protein Donor)	false