scPDB - 2c3y entry

Protein Data Bank Entry:

PDB ID : 2c3y

Resolution :1.930 Å

Experimental Method : X-ray

Deposition Date : 2005-10-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pyruvate synthase
ID:	POR_DESAF
AC:	P94692
Organism:	Desulfovibrio africanus
Reign:	Bacteria
TaxID:	873
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	4 %
B	96 %

Ligand binding site composition:

B-Factor:	11.626
Number of residues:	57
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	2
Water Molecules:	7
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.799	313.875

% Hydrophobic	% Polar
64.52	35.48
According to VolSite

Ligand :

HET Code:	HTL
Formula:	C14H18N4O8P2S
Molecular weight:	464.327 g/mol
DrugBank ID:	DB02410
Buried Surface Area:	84.42 %
Polar Surface area:	242.39 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-18.1831	-41.6579	30.8567

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
C5'	CD1	ILE- 30	3.67	0	Hydrophobic	false
C35	CG1	ILE- 30	3.69	0	Hydrophobic	false
N1'	OE2	GLU- 64	2.95	148.65	H-Bond (Ligand Donor)	false
C2A	CB	GLN- 88	3.9	0	Hydrophobic	false
C2A	CD1	LEU- 92	3.46	0	Hydrophobic	false
O2'	NH2	ARG- 114	3.19	159.9	H-Bond (Protein Donor)	false
C3'	CD1	LEU- 121	4.07	0	Hydrophobic	false
C3'	CG2	ILE- 123	4.42	0	Hydrophobic	false
O21	OE2	GLU- 817	2.61	155.72	H-Bond (Protein Donor)	false
S1	CG2	THR- 838	4.08	0	Hydrophobic	false
C3'	CG2	THR- 838	3.48	0	Hydrophobic	false
O22	N	CYS- 840	2.88	164.87	H-Bond (Protein Donor)	false
C3'	CD1	ILE- 843	3.91	0	Hydrophobic	false
C5B	CE1	PHE- 869	3.53	0	Hydrophobic	false
C5	CZ	PHE- 869	4.03	0	Hydrophobic	false
O12	N	GLY- 964	2.76	155.61	H-Bond (Protein Donor)	false
O13	N	TRP- 965	2.87	146.51	H-Bond (Protein Donor)	false
C2A	CD1	ILE- 969	3.77	0	Hydrophobic	false
C5B	CD2	TYR- 994	3.78	0	Hydrophobic	false
O23	N	SER- 995	2.88	156.83	H-Bond (Protein Donor)	false
S1	CB	ASN- 996	3.78	0	Hydrophobic	false
C5A	CB	ASN- 996	4.17	0	Hydrophobic	false
O22	N	ASN- 996	3.03	169.31	H-Bond (Protein Donor)	false
C35	CG2	THR- 997	3.9	0	Hydrophobic	false
C5A	CG2	THR- 997	4.25	0	Hydrophobic	false
S1	CG2	THR- 997	4.01	0	Hydrophobic	false
C3'	SD	MET- 1202	4.26	0	Hydrophobic	false
O12	MG	MG- 2237	2.03	0	Metal Acceptor	false
O23	MG	MG- 2237	1.98	0	Metal Acceptor	false
O21	O	HOH- 2814	2.8	160.77	H-Bond (Protein Donor)	false
N3'	O	HOH- 2840	2.88	162.83	H-Bond (Protein Donor)	false
O21	O	HOH- 2927	2.99	138.2	H-Bond (Protein Donor)	false
O13	O	HOH- 3097	2.72	179.97	H-Bond (Protein Donor)	false