scPDB - 1c7o entry

Protein Data Bank Entry:

PDB ID : 1c7o

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2000-03-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Hemolysin
ID:	Q56257_TREDN
AC:	Q56257
Organism:	Treponema denticola
Reign:	Bacteria
TaxID:	158
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
G	92 %
H	8 %

Ligand binding site composition:

B-Factor:	28.100
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.835	1717.875

% Hydrophobic	% Polar
57.96	42.04
According to VolSite

Ligand :

HET Code:	PPG
Formula:	C14H18N3O8P
Molecular weight:	387.282 g/mol
DrugBank ID:	DB03287
Buried Surface Area:	70.88 %
Polar Surface area:	204.7 Å2

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

Mass center Coordinates

X	Y	Z
33.6033	59.0638	136.128

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
CBI	CG1	VAL- 38	3.7	0	Hydrophobic	false
C4A	CB	ALA- 39	4.3	0	Hydrophobic	false
CBI	CB	ALA- 39	3.98	0	Hydrophobic	false
O2B	N	ALA- 39	2.88	147.95	H-Bond (Protein Donor)	false
CGI	CE2	TYR- 64	3.62	0	Hydrophobic	false
OP1	N	VAL- 98	3.34	120.26	H-Bond (Protein Donor)	false
OP2	N	VAL- 98	3.2	175.57	H-Bond (Protein Donor)	false
OP1	N	VAL- 99	3.39	173.47	H-Bond (Protein Donor)	false
C5A	CG2	VAL- 99	3.93	0	Hydrophobic	false
C2A	CD2	TYR- 123	3.95	0	Hydrophobic	false
C4A	CZ	TYR- 123	3.85	0	Hydrophobic	false
C5A	CE2	TYR- 123	4.28	0	Hydrophobic	false
N4A	OH	TYR- 123	2.97	153.69	H-Bond (Ligand Donor)	false
C2A	SG	CYS- 171	3.37	0	Hydrophobic	false
O3	ND2	ASN- 175	2.84	136.09	H-Bond (Protein Donor)	false
O3B	ND2	ASN- 175	3.4	129.17	H-Bond (Protein Donor)	false
N1	OD1	ASP- 203	2.59	170.9	H-Bond (Ligand Donor)	false
C2A	CG2	ILE- 205	4.12	0	Hydrophobic	false
C3	CG2	ILE- 205	3.9	0	Hydrophobic	false
C5	CD1	ILE- 205	3.87	0	Hydrophobic	false
OP3	NZ	LYS- 238	3.73	0	Ionic (Protein Cationic)	false
O2B	NH2	ARG- 369	2.75	171.81	H-Bond (Protein Donor)	false
O2B	NH1	ARG- 369	3.44	129.75	H-Bond (Protein Donor)	false
O3B	NH1	ARG- 369	2.78	164.15	H-Bond (Protein Donor)	false