scPDB - 3zkp entry

Protein Data Bank Entry:

PDB ID : 3zkp

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2013-01-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Erythromycin C-12 hydroxylase
ID:	ERYK_SACEN
AC:	P48635
Organism:	Saccharopolyspora erythraea
Reign:	Bacteria
TaxID:	405948
EC Number:	1.14.13.154

Chains:

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

Ligand binding site composition:

B-Factor:	13.285
Number of residues:	44
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.736	1842.750

% Hydrophobic	% Polar
54.40	45.60
According to VolSite

Ligand :

HET Code:	ERB
Formula:	C37H68NO12
Molecular weight:	718.935 g/mol
DrugBank ID:	-
Buried Surface Area:	62.59 %
Polar Surface area:	174.88 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	5
Rings:	3
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
13.0808	-4.60986	28.4934

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
C20	CG2	THR- 83	4.16	0	Hydrophobic	false
C20	CB	ALA- 86	3.74	0	Hydrophobic	false
C37	CG2	ILE- 87	4.49	0	Hydrophobic	false
C36	CB	HIS- 88	3.92	0	Hydrophobic	false
O6	OE2	GLU- 89	2.62	168.81	H-Bond (Ligand Donor)	false
C27	CD1	LEU- 169	3.95	0	Hydrophobic	false
C32	CD2	LEU- 169	3.77	0	Hydrophobic	false
C27	CG2	ILE- 172	3.98	0	Hydrophobic	false
C25	SD	MET- 174	3.78	0	Hydrophobic	false
C21	CD1	ILE- 186	4.1	0	Hydrophobic	false
C27	CD1	ILE- 186	3.68	0	Hydrophobic	false
C15	CG2	ILE- 186	3.69	0	Hydrophobic	false
C15	CD1	LEU- 190	3.69	0	Hydrophobic	false
C19	CD1	LEU- 190	4.34	0	Hydrophobic	false
C30	CB	ALA- 237	3.97	0	Hydrophobic	false
C37	CB	ALA- 237	3.88	0	Hydrophobic	false
C30	CD1	LEU- 240	3.96	0	Hydrophobic	false
C37	CB	ALA- 241	3.65	0	Hydrophobic	false
C33	CG2	ILE- 244	3.76	0	Hydrophobic	false
C34	CG2	THR- 245	3.69	0	Hydrophobic	false
C23	CE1	PHE- 288	4.47	0	Hydrophobic	false
C35	CE2	PHE- 288	4.12	0	Hydrophobic	false
C7	CE1	PHE- 288	3.73	0	Hydrophobic	false
C34	CD2	PHE- 288	3.5	0	Hydrophobic	false
N1	OE1	GLN- 292	2.95	147.1	H-Bond (Ligand Donor)	false
C32	CG2	ILE- 392	3.98	0	Hydrophobic	false
C27	CD1	ILE- 392	3.87	0	Hydrophobic	false
C33	CG1	VAL- 393	3.89	0	Hydrophobic	false
O12	O	HOH- 2212	2.77	130.75	H-Bond (Ligand Donor)	false
O8	O	HOH- 2248	2.92	179.97	H-Bond (Protein Donor)	false