scPDB - 5e7o entry

Protein Data Bank Entry:

PDB ID : 5e7o

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2015-10-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DMSO reductase family type II enzyme, molybdopterin subunit
ID:	G8QM55_DECSP
AC:	G8QM55
Organism:	Dechlorosoma suillum
Reign:	Bacteria
TaxID:	640081
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	31.097
Number of residues:	66
Including
Standard Amino Acids:	64
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.104	351.000

% Hydrophobic	% Polar
34.62	65.38
According to VolSite

Ligand :

HET Code:	MD1
Formula:	C20H24N10O13P2S2
Molecular weight:	738.541 g/mol
DrugBank ID:	-
Buried Surface Area:	79.4 %
Polar Surface area:	452.26 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	10
Rings:	5
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-82.1428	-124.587	434.882

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
C10	CZ	TYR- 168	3.69	0	Hydrophobic	false
C11	CD1	TYR- 168	3.69	0	Hydrophobic	false
S12	CD2	TYR- 168	3.43	0	Hydrophobic	false
S13	CB	TYR- 168	3.44	0	Hydrophobic	false
C14	CB	TYR- 168	4.34	0	Hydrophobic	false
C7	CD1	TYR- 168	4.02	0	Hydrophobic	false
O2B	N	ASN- 539	2.71	145.93	H-Bond (Protein Donor)	false
C5'	CB	ASN- 539	4.3	0	Hydrophobic	false
C10	CG	GLN- 543	4.47	0	Hydrophobic	false
C11	CB	GLN- 543	4.3	0	Hydrophobic	false
C7	CB	GLN- 543	4.37	0	Hydrophobic	false
O11	NE2	GLN- 543	2.56	149.41	H-Bond (Protein Donor)	false
N8	O	GLN- 543	3.31	162.54	H-Bond (Ligand Donor)	false
N2	O	ILE- 564	2.63	158.34	H-Bond (Ligand Donor)	false
O2'	OD1	ASN- 565	2.94	178.96	H-Bond (Ligand Donor)	false
O3'	ND2	ASN- 565	3.21	157.09	H-Bond (Protein Donor)	false
O2'	NE	ARG- 567	3.02	133.32	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 569	2.89	122.84	H-Bond (Ligand Donor)	false
N7	NE1	TRP- 584	2.93	167.22	H-Bond (Protein Donor)	false
O6	NZ	LYS- 587	3.1	151.08	H-Bond (Protein Donor)	false
N2	OD1	ASP- 615	2.9	155.98	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 615	2.79	150.89	H-Bond (Ligand Donor)	false
N1	OD1	ASP- 615	3.31	137.8	H-Bond (Ligand Donor)	false
O14	O	SER- 762	3.02	157.73	H-Bond (Ligand Donor)	false
N16	OG	SER- 762	2.89	137.87	H-Bond (Ligand Donor)	false
C10	CB	HIS- 770	4.25	0	Hydrophobic	false
O11	ND1	HIS- 770	3.09	172.47	H-Bond (Ligand Donor)	false
O2A	OG	SER- 771	2.64	157.68	H-Bond (Protein Donor)	false
O2A	N	SER- 771	2.96	161.76	H-Bond (Protein Donor)	false
O1A	OG1	THR- 772	2.69	145.5	H-Bond (Protein Donor)	false
O1A	N	THR- 772	3.4	150.15	H-Bond (Protein Donor)	false
C16	CB	HIS- 835	3.97	0	Hydrophobic	false
N16	OE1	GLN- 849	2.64	133.51	H-Bond (Ligand Donor)	false
O14	NE2	GLN- 881	3.07	165.42	H-Bond (Protein Donor)	false