scPDB - 3slk entry

Protein Data Bank Entry:

PDB ID : 3slk

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2011-06-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Polyketide synthase extender module 2
ID:	Q9ALM5_9PSEU
AC:	Q9ALM5
Organism:	Saccharopolyspora spinosa
Reign:	Bacteria
TaxID:	60894
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	96.176
Number of residues:	46
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.288	1171.125

% Hydrophobic	% Polar
50.14	49.86
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	53.14 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
14.2332	98.4164	23.9255

Binding mode :

What is Poseview ?

2D View
3D View

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
C5B	CD1	PHE- 231	3.72	0	Hydrophobic	false
C3D	CB	PHE- 231	3.55	0	Hydrophobic	false
C5N	CG2	ILE- 307	3.96	0	Hydrophobic	false
C1B	CB	SER- 332	4.18	0	Hydrophobic	false
C4B	CB	SER- 332	3.71	0	Hydrophobic	false
O2A	N	GLY- 336	3.3	158.91	H-Bond (Protein Donor)	false
O2N	N	VAL- 337	2.92	172.19	H-Bond (Protein Donor)	false
C5D	CB	VAL- 337	4.35	0	Hydrophobic	false
C5N	CG2	VAL- 337	4.05	0	Hydrophobic	false
O2X	N	SER- 357	3.18	143.49	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 360	3.22	141.84	H-Bond (Protein Donor)	false
O3X	NZ	LYS- 360	3.52	0	Ionic (Protein Cationic)	false
O1X	OG	SER- 374	2.95	151.08	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 375	3.87	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 375	3.34	0	Ionic (Protein Cationic)	false
O3X	NH1	ARG- 375	2.94	132.76	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 375	2.94	132.67	H-Bond (Protein Donor)	false
C4D	CB	SER- 398	4.04	0	Hydrophobic	false
C3N	CD2	LEU- 420	4.4	0	Hydrophobic	false
N7N	OD2	ASP- 444	3.08	128.34	H-Bond (Ligand Donor)	false
O7N	N	THR- 445	3.04	170.93	H-Bond (Protein Donor)	false
O7N	OG1	THR- 445	3.02	165.56	H-Bond (Protein Donor)	false
C3B	CB	ALA- 492	3.91	0	Hydrophobic	false
O2A	NE2	HIS- 494	3	145.96	H-Bond (Protein Donor)	false