scPDB - 4l80 entry

Protein Data Bank Entry:

PDB ID : 4l80

Resolution :2.010 Å

Experimental Method : X-ray

Deposition Date : 2013-06-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Malyl-CoA/beta-methylmalyl-CoA/citramalyl-CoA lyase
ID:	MCLA_CHLAU
AC:	S5N020
Organism:	Chloroflexus aurantiacus
Reign:	Bacteria
TaxID:	1108
EC Number:	4.1.3.24

Chains:

Chain Name:	Percentage of Residues within binding site
D	24 %
E	76 %

Ligand binding site composition:

B-Factor:	29.908
Number of residues:	43
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.788	489.375

% Hydrophobic	% Polar
59.31	40.69
According to VolSite

Ligand :

HET Code:	1VU
Formula:	C24H36N7O17P3S
Molecular weight:	819.566 g/mol
DrugBank ID:	DB02912
Buried Surface Area:	49.57 %
Polar Surface area:	429.68 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	21

Mass center Coordinates

X	Y	Z
-26.3632	-43.7258	30.4687

Binding mode :

What is Poseview ?

2D View
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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
N5	NE2	HIS- 32	2.91	150.79	H-Bond (Protein Donor)	false
N4	O	PHE- 33	2.7	157.75	H-Bond (Ligand Donor)	false
C3	CD2	PHE- 33	4.11	0	Hydrophobic	false
O14	NZ	LYS- 40	3.27	154.74	H-Bond (Protein Donor)	false
O14	NZ	LYS- 40	3.27	0	Ionic (Protein Cationic)	false
O16	NZ	LYS- 40	2.93	0	Ionic (Protein Cationic)	false
C16	CD1	ILE- 41	4.02	0	Hydrophobic	false
C6	CB	ALA- 62	4.44	0	Hydrophobic	false
O	NH2	ARG- 92	3.06	165.56	H-Bond (Protein Donor)	false
C	CB	ALA- 183	3.81	0	Hydrophobic	false
C	CG1	VAL- 196	3.97	0	Hydrophobic	false
S	CB	PRO- 246	3.87	0	Hydrophobic	false
C	CG	PRO- 246	4.17	0	Hydrophobic	false
O9	NZ	LYS- 251	3.66	0	Ionic (Protein Cationic)	false
C3	CZ3	TRP- 272	3.88	0	Hydrophobic	false
N4	O	LEU- 274	3.34	138.27	H-Bond (Ligand Donor)	false
N1	O	LEU- 274	3.08	144.39	H-Bond (Ligand Donor)	false
C6	CB	LEU- 274	4.36	0	Hydrophobic	false
C3	CD2	LEU- 274	3.74	0	Hydrophobic	false
C16	CG	PRO- 276	4.36	0	Hydrophobic	false
C11	CG2	VAL- 309	4.23	0	Hydrophobic	false
C12	CG2	VAL- 309	4.3	0	Hydrophobic	false
C13	CE	MET- 311	3.43	0	Hydrophobic	false
C11	CG	MET- 316	3.77	0	Hydrophobic	false
C6	CE	MET- 316	4.06	0	Hydrophobic	false
S	CE	MET- 316	4.49	0	Hydrophobic	false
C1	CB	ALA- 320	3.94	0	Hydrophobic	false