scPDB - 4d9f entry

Protein Data Bank Entry:

PDB ID : 4d9f

Resolution :2.610 Å

Experimental Method : X-ray

Deposition Date : 2012-01-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	D-cysteine desulfhydrase
ID:	DCYD_SALTY
AC:	Q8ZNT7
Organism:	Salmonella typhimurium
Reign:	Bacteria
TaxID:	99287
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	39.581
Number of residues:	40
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.439	661.500

% Hydrophobic	% Polar
43.37	56.63
According to VolSite

Ligand :

HET Code:	DCS
Formula:	C11H15N3O7P
Molecular weight:	332.226 g/mol
DrugBank ID:	DB02038
Buried Surface Area:	75.59 %
Polar Surface area:	170.29 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	3
Rings:	2
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
23.4386	72.3395	9.191

Binding mode :

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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
O1P	NZ	LYS- 51	3.44	136.43	H-Bond (Protein Donor)	false
O1P	NZ	LYS- 51	3.44	0	Ionic (Protein Cationic)	false
O2P	NZ	LYS- 51	3.33	0	Ionic (Protein Cationic)	false
O3	ND2	ASN- 79	2.97	160.58	H-Bond (Protein Donor)	false
O3P	N	GLY- 194	3.03	141.7	H-Bond (Protein Donor)	false
O1P	OG	SER- 195	2.5	145.69	H-Bond (Protein Donor)	false
O1P	N	SER- 195	2.79	133.45	H-Bond (Protein Donor)	false
CB	CB	SER- 195	4.49	0	Hydrophobic	false
O3P	N	ALA- 196	2.97	121.04	H-Bond (Protein Donor)	false
O4P	OG1	THR- 198	3.34	150.17	H-Bond (Protein Donor)	false
O2P	N	THR- 198	2.73	145.18	H-Bond (Protein Donor)	false
O2P	OG1	THR- 198	2.63	140.46	H-Bond (Protein Donor)	false
CB	CE1	TYR- 261	4.34	0	Hydrophobic	false
C2A	CD2	TYR- 287	3.75	0	Hydrophobic	false
C3	CB	TYR- 287	4.41	0	Hydrophobic	false
C5A	CD1	TYR- 287	4.16	0	Hydrophobic	false
CB	CE1	TYR- 287	3.68	0	Hydrophobic	false
DuAr	DuAr	TYR- 287	3.66	0	Aromatic Face/Face	false
C2A	CB	THR- 315	4.05	0	Hydrophobic	false