scPDB - 2bm9 entry

Protein Data Bank Entry:

PDB ID : 2bm9

Resolution :2.940 Å

Experimental Method : X-ray

Deposition Date : 2005-03-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cephalosporin hydroxylase CmcI
ID:	O85726_STRCL
AC:	O85726
Organism:	Streptomyces clavuligerus
Reign:	Bacteria
TaxID:	1901
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	9.378
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.081	486.000

% Hydrophobic	% Polar
44.44	55.56
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	62.11 %
Polar Surface area:	189.77 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
48.7123	60.4144	69.0201

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
SD	CD2	LEU- 18	3.6	0	Hydrophobic	false
O	NZ	LYS- 65	3.45	140.57	H-Bond (Protein Donor)	false
O	NZ	LYS- 65	3.45	0	Ionic (Protein Cationic)	false
N	OE2	GLU- 87	3.17	122.98	H-Bond (Ligand Donor)	false
N	OE2	GLU- 87	3.17	0	Ionic (Ligand Cationic)	false
N	OE1	GLU- 87	3.57	0	Ionic (Ligand Cationic)	false
N	O	GLY- 89	3.23	125.2	H-Bond (Ligand Donor)	false
O3'	N	TYR- 91	3.05	122.69	H-Bond (Protein Donor)	false
CG	CB	TYR- 91	4.3	0	Hydrophobic	false
O3'	OD2	ASP- 116	2.68	156.16	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 116	3.19	164.31	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 116	2.6	132.22	H-Bond (Ligand Donor)	false
O3'	NH2	ARG- 121	3.37	146.85	H-Bond (Protein Donor)	false
O3'	NH1	ARG- 121	3.43	144.5	H-Bond (Protein Donor)	false
O2'	NH2	ARG- 121	3.26	135.39	H-Bond (Protein Donor)	false
N6	OD2	ASP- 138	2.92	120.51	H-Bond (Ligand Donor)	false
N1	N	CYS- 139	3.18	134.08	H-Bond (Protein Donor)	false
CE	CB	ASN- 160	4.34	0	Hydrophobic	false
CG	CB	ASN- 160	3.93	0	Hydrophobic	false
C1'	CB	ALA- 161	4.19	0	Hydrophobic	false
N	O	HOH- 2025	3.03	130.64	H-Bond (Ligand Donor)	false