scPDB - 3nyr entry

Protein Data Bank Entry:

PDB ID : 3nyr

Resolution :1.450 Å

Experimental Method : X-ray

Deposition Date : 2010-07-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative fatty acid synthase
ID:	Q9L0A2_STRCO
AC:	Q9L0A2
Organism:	Streptomyces coelicolor / M145)
Reign:	Bacteria
TaxID:	100226
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	12.194
Number of residues:	39
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:	AMP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.789	658.125

% Hydrophobic	% Polar
43.59	56.41
According to VolSite

Ligand :

HET Code:	MLC
Formula:	C24H33N7O19P3S
Molecular weight:	848.541 g/mol
DrugBank ID:	DB04524
Buried Surface Area:	65.67 %
Polar Surface area:	469.81 Å2

Number of
H-Bond Acceptors:	24
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	22

Mass center Coordinates

X	Y	Z
14.7917	4.08582	58.8921

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
CP4	CG	PRO- 184	3.99	0	Hydrophobic	false
CP1	CB	HIS- 187	3.75	0	Hydrophobic	false
CM2	CG2	VAL- 188	4.22	0	Hydrophobic	false
CP8	CG2	VAL- 230	3.95	0	Hydrophobic	false
CP4	CG1	VAL- 230	4.33	0	Hydrophobic	false
CPB	CG2	THR- 232	4.24	0	Hydrophobic	false
CP8	CG2	THR- 232	3.71	0	Hydrophobic	false
CP9	CE	MET- 233	4.37	0	Hydrophobic	false
CP8	CE	MET- 233	4.23	0	Hydrophobic	false
O22	CZ	ARG- 236	3.59	0	Ionic (Protein Cationic)	false
O22	NH2	ARG- 236	2.7	173.51	H-Bond (Protein Donor)	false
S	CB	SER- 261	3.77	0	Hydrophobic	false
OM3	OG	SER- 261	2.63	151.58	H-Bond (Protein Donor)	false
OM3	CZ	ARG- 283	3.87	0	Ionic (Protein Cationic)	false
OM4	CZ	ARG- 283	3.7	0	Ionic (Protein Cationic)	false
OM3	NH2	ARG- 283	3.02	159.09	H-Bond (Protein Donor)	false
OM4	NH1	ARG- 283	3	163.4	H-Bond (Protein Donor)	false
NP2	O	GLY- 392	2.79	148.68	H-Bond (Ligand Donor)	false
NP1	O	GLY- 393	2.98	157.72	H-Bond (Ligand Donor)	false
CP7	CE2	TYR- 394	3.84	0	Hydrophobic	false
CP4	CD2	TYR- 394	3.71	0	Hydrophobic	false
O21	CZ	ARG- 461	3.91	0	Ionic (Protein Cationic)	false
O21	NH2	ARG- 461	2.86	154.79	H-Bond (Protein Donor)	false
CM2	C5'	AMP- 487	4.08	0	Hydrophobic	false
OM2	O	HOH- 500	3.47	128	H-Bond (Protein Donor)	false
OP1	O	HOH- 503	2.8	154.04	H-Bond (Protein Donor)	false