scPDB - 4ydd entry

Protein Data Bank Entry:

PDB ID : 4ydd

Resolution :1.860 Å

Experimental Method : X-ray

Deposition Date : 2015-02-21

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
A	100 %

Ligand binding site composition:

B-Factor:	16.197
Number of residues:	71
Including
Standard Amino Acids:	63
Non Standard Amino Acids:	1
Water Molecules:	7
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.717	739.125

% Hydrophobic	% Polar
40.64	59.36
According to VolSite

Ligand :

HET Code:	MGD
Formula:	C20H24N10O13P2S2
Molecular weight:	738.541 g/mol
DrugBank ID:	-
Buried Surface Area:	81.77 %
Polar Surface area:	440.93 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	10
Rings:	6
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
184.352	192.118	209.583

Binding mode :

What is Poseview ?

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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
O1A	N	ASN- 203	2.94	150.37	H-Bond (Protein Donor)	false
C5'	CB	ASN- 203	3.67	0	Hydrophobic	false
N19	O	GLN- 206	2.97	120.31	H-Bond (Ligand Donor)	false
O1A	OG1	THR- 207	2.73	166.04	H-Bond (Protein Donor)	false
C10	CB	THR- 207	4.48	0	Hydrophobic	false
C23	CB	THR- 207	4.26	0	Hydrophobic	false
N22	O	THR- 207	2.65	153.96	H-Bond (Ligand Donor)	false
N2	O	ILE- 228	2.72	163	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 231	3.46	164.98	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 231	2.67	127.71	H-Bond (Ligand Donor)	false
O3'	ND2	ASN- 233	3.03	155.02	H-Bond (Protein Donor)	false
O6	N	GLY- 248	2.96	154.96	H-Bond (Protein Donor)	false
N1	OD1	ASP- 250	2.6	169.2	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 250	2.87	165.57	H-Bond (Ligand Donor)	false
O2A	N	GLY- 422	2.89	169.44	H-Bond (Protein Donor)	false
S12	CG2	ILE- 458	3.6	0	Hydrophobic	false
O2'	ND2	ASN- 761	3.13	135.26	H-Bond (Protein Donor)	false
C3'	CB	PRO- 763	4.42	0	Hydrophobic	false
O1B	N	HIS- 764	2.95	170.62	H-Bond (Protein Donor)	false
C10	CB	HIS- 764	4.29	0	Hydrophobic	false
N18	O	SER- 768	2.59	147.99	H-Bond (Ligand Donor)	false
N19	O	SER- 768	3.47	121.31	H-Bond (Ligand Donor)	false
O17	N	HIS- 770	2.73	158.98	H-Bond (Protein Donor)	false
O2'	NH2	ARG- 830	3.21	177.93	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 882	2.63	154.66	H-Bond (Protein Donor)	false
O2B	NH1	ARG- 882	2.97	134.46	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 882	3.21	0	Ionic (Protein Cationic)	false
O2A	O	HOH- 1145	2.53	179.97	H-Bond (Protein Donor)	false
O1B	O	HOH- 1217	2.64	163.75	H-Bond (Protein Donor)	false
O17	O	HOH- 1388	2.79	179.96	H-Bond (Protein Donor)	false