scPDB - 4l9y entry

Protein Data Bank Entry:

PDB ID : 4l9y

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2013-06-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	L-malyl-CoA/beta-methylmalyl-CoA lyase
ID:	MCAL_RHOS4
AC:	Q3J5L6
Organism:	Rhodobacter sphaeroides
Reign:	Bacteria
TaxID:	272943
EC Number:	4.1.3.24

Chains:

Chain Name:	Percentage of Residues within binding site
A	28 %
B	72 %

Ligand binding site composition:

B-Factor:	30.425
Number of residues:	44
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.918	543.375

% Hydrophobic	% Polar
61.49	38.51
According to VolSite

Ligand :

HET Code:	1VU
Formula:	C24H36N7O17P3S
Molecular weight:	819.566 g/mol
DrugBank ID:	DB02912
Buried Surface Area:	53.1 %
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
15.5678	80.3453	82.0078

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
N4	O	PHE- 19	2.97	150.05	H-Bond (Ligand Donor)	false
C3	CD2	PHE- 19	3.93	0	Hydrophobic	false
O6	CZ	ARG- 24	3.78	0	Ionic (Protein Cationic)	false
O6	NH1	ARG- 24	3.02	167.5	H-Bond (Protein Donor)	false
C22	CD2	LEU- 27	4.33	0	Hydrophobic	false
O15	NZ	LYS- 30	3.62	0	Ionic (Protein Cationic)	false
O16	NZ	LYS- 30	3.21	0	Ionic (Protein Cationic)	false
O13	NZ	LYS- 30	3.47	149.93	H-Bond (Protein Donor)	false
C16	CD	LYS- 30	4.26	0	Hydrophobic	false
C6	CB	SER- 46	4.36	0	Hydrophobic	false
O	NH1	ARG- 76	3.24	139.42	H-Bond (Protein Donor)	false
O	NH2	ARG- 76	2.93	157.5	H-Bond (Protein Donor)	false
C	CB	ALA- 167	3.49	0	Hydrophobic	false
C	CD1	ILE- 180	3.59	0	Hydrophobic	false
S	CB	PRO- 223	4.17	0	Hydrophobic	false
C	CG	PRO- 223	3.75	0	Hydrophobic	false
C3	CZ3	TRP- 249	3.71	0	Hydrophobic	false
N1	O	ILE- 251	2.79	133.04	H-Bond (Ligand Donor)	false
C6	CB	ILE- 251	4.33	0	Hydrophobic	false
C3	CG2	ILE- 251	3.81	0	Hydrophobic	false
O9	NE2	HIS- 252	3.15	165.19	H-Bond (Protein Donor)	false
C16	CG	PRO- 253	4.03	0	Hydrophobic	false
C12	CB	ALA- 290	4.5	0	Hydrophobic	false
C6	CB	ALA- 290	4.48	0	Hydrophobic	false
C13	CG2	VAL- 292	3.95	0	Hydrophobic	false
C11	CG2	VAL- 292	4.26	0	Hydrophobic	false
C11	CD1	LEU- 297	3.85	0	Hydrophobic	false
C6	CD1	LEU- 297	4.19	0	Hydrophobic	false
S	CD2	LEU- 297	3.84	0	Hydrophobic	false
C	CD2	LEU- 297	4.22	0	Hydrophobic	false
C1	CB	ALA- 301	4.03	0	Hydrophobic	false