scPDB - 1r00 entry

Protein Data Bank Entry:

PDB ID : 1r00

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2003-09-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aclacinomycin 10-hydroxylase RdmB
ID:	RDMB_STREF
AC:	Q54527
Organism:	Streptomyces purpurascens
Reign:	Bacteria
TaxID:	1924
EC Number:	4.1.1

Chains:

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

Ligand binding site composition:

B-Factor:	27.088
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.971	1667.250

% Hydrophobic	% Polar
56.07	43.93
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	69.23 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
21.4831	26.8638	42.8444

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	CH2	TRP- 146	3.63	0	Hydrophobic	false
C5'	CZ2	TRP- 146	3.96	0	Hydrophobic	false
C2'	CE3	TRP- 146	3.57	0	Hydrophobic	false
O	OH	TYR- 171	2.78	127.86	H-Bond (Protein Donor)	false
OXT	OH	TYR- 171	2.91	124.32	H-Bond (Protein Donor)	false
N	O	GLY- 190	2.79	162.27	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 213	3.4	138.8	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 213	2.7	162.26	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 213	2.7	154.96	H-Bond (Ligand Donor)	false
C2'	CD1	LEU- 214	4.45	0	Hydrophobic	false
N6	OD1	ASP- 240	2.8	160.5	H-Bond (Ligand Donor)	false
C1'	CE2	PHE- 241	4.2	0	Hydrophobic	false
N1	N	PHE- 241	3	167.98	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 241	3.39	0	Aromatic Face/Face	false
N	O	SER- 255	2.69	160.2	H-Bond (Ligand Donor)	false
O	OG	SER- 255	2.73	160.23	H-Bond (Protein Donor)	false
CB	CG2	VAL- 257	4.27	0	Hydrophobic	false