scPDB - 2vzz entry

Protein Data Bank Entry:

PDB ID : 2vzz

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2008-08-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative succinyl-CoA transferase Rv0802c
ID:	Y802_MYCTU
AC:	P9WQG7
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	2.8.3

Chains:

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

Ligand binding site composition:

B-Factor:	11.652
Number of residues:	44
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.123	732.375

% Hydrophobic	% Polar
42.86	57.14
According to VolSite

Ligand :

HET Code:	SCA
Formula:	C25H35N7O19P3S
Molecular weight:	862.567 g/mol
DrugBank ID:	DB03699
Buried Surface Area:	56.69 %
Polar Surface area:	469.81 Å2

Number of
H-Bond Acceptors:	24
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	23

Mass center Coordinates

X	Y	Z
17.4394	44.7112	6.07764

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
CP4	CG1	VAL- 38	4.32	0	Hydrophobic	false
CP4	CG	PRO- 45	3.74	0	Hydrophobic	false
CP1	CB	PRO- 45	4.35	0	Hydrophobic	false
CP4	CZ	PHE- 46	3.52	0	Hydrophobic	false
CP1	CD2	PHE- 46	4.28	0	Hydrophobic	false
OS5	NE2	GLN- 94	3.23	161	H-Bond (Protein Donor)	false
OS4	OG	SER- 109	2.56	158.82	H-Bond (Protein Donor)	false
CP8	CB	SER- 111	4.16	0	Hydrophobic	false
NP1	O	SER- 111	2.96	140.93	H-Bond (Ligand Donor)	false
OS1	N	SER- 111	3.12	147.94	H-Bond (Protein Donor)	false
CP4	CB	TRP- 112	4.13	0	Hydrophobic	false
CP8	CD1	LEU- 113	4.24	0	Hydrophobic	false
OP2	N	LEU- 113	2.63	144.05	H-Bond (Protein Donor)	false
CP7	CG	GLN- 118	3.64	0	Hydrophobic	false
O22	N	GLY- 119	3.15	142.75	H-Bond (Protein Donor)	false
O11	N	GLY- 121	2.87	147.89	H-Bond (Protein Donor)	false
O21	N	GLY- 123	2.91	142.23	H-Bond (Protein Donor)	false
O12	N	THR- 124	2.91	150.55	H-Bond (Protein Donor)	false
O12	OG1	THR- 124	2.9	156.3	H-Bond (Protein Donor)	false
CP8	CE	MET- 126	3.99	0	Hydrophobic	false
OS4	CZ	ARG- 127	3.37	0	Ionic (Protein Cationic)	false
OS5	CZ	ARG- 127	3.78	0	Ionic (Protein Cationic)	false
OS4	OG	SER- 145	2.86	163.63	H-Bond (Protein Donor)	false
CPB	CB	ALA- 153	4.19	0	Hydrophobic	false
CP9	CB	ALA- 153	4.25	0	Hydrophobic	false
CP9	CB	SER- 154	3.86	0	Hydrophobic	false
S	CB	SER- 154	4.01	0	Hydrophobic	false
CS3	CB	SER- 154	4.31	0	Hydrophobic	false
C1'	CB	ALA- 156	3.99	0	Hydrophobic	false
C4'	CB	ALA- 156	3.48	0	Hydrophobic	false
C5'	CG2	VAL- 157	4.19	0	Hydrophobic	false
CPB	CG2	VAL- 157	3.94	0	Hydrophobic	false
O31	CZ	ARG- 160	3.93	0	Ionic (Protein Cationic)	false
O33	CZ	ARG- 160	3.78	0	Ionic (Protein Cationic)	false
O33	NE	ARG- 160	2.87	120.57	H-Bond (Protein Donor)	false
O21	O	HOH- 2127	2.52	152.47	H-Bond (Protein Donor)	false