scPDB - 2h12 entry

Protein Data Bank Entry:

PDB ID : 2h12

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2006-05-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Citrate synthase
ID:	CISY_ACEAC
AC:	P20901
Organism:	Acetobacter aceti
Reign:	Bacteria
TaxID:	435
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	10 %
B	90 %

Ligand binding site composition:

B-Factor:	23.252
Number of residues:	42
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.810	745.875

% Hydrophobic	% Polar
47.51	52.49
According to VolSite

Ligand :

HET Code:	CMX
Formula:	C23H33N7O18P3
Molecular weight:	788.466 g/mol
DrugBank ID:	-
Buried Surface Area:	57.16 %
Polar Surface area:	427.44 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	20

Mass center Coordinates

X	Y	Z
-0.632373	-46.5494	-29.0467

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
CEP	CB	ALA- 271	4.18	0	Hydrophobic	false
N4P	O	ALA- 271	3.02	155.89	H-Bond (Ligand Donor)	false
O21	ND1	HIS- 272	2.67	156.48	H-Bond (Protein Donor)	false
C6P	CB	ALA- 275	4.19	0	Hydrophobic	false
N1A	N	LEU- 308	3.16	165.14	H-Bond (Protein Donor)	false
N6A	O	LEU- 308	2.95	162.21	H-Bond (Ligand Donor)	false
C6P	CE	MET- 309	3.93	0	Hydrophobic	false
O5P	N	GLY- 310	2.76	142.39	H-Bond (Protein Donor)	false
N6A	O	PHE- 311	2.99	122.9	H-Bond (Ligand Donor)	false
N8P	O	PHE- 311	2.99	131.65	H-Bond (Ligand Donor)	false
O4A	CZ	ARG- 314	3.55	0	Ionic (Protein Cationic)	false
O5A	CZ	ARG- 314	3.74	0	Ionic (Protein Cationic)	false
O4A	NE	ARG- 314	2.6	163.08	H-Bond (Protein Donor)	false
O5A	NH2	ARG- 314	2.91	169.36	H-Bond (Protein Donor)	false
N3A	OH	TYR- 360	2.78	171.67	H-Bond (Protein Donor)	false
C1B	CD	ARG- 364	3.89	0	Hydrophobic	false
C4B	CD	ARG- 364	3.92	0	Hydrophobic	false
O3B	NE	ARG- 364	3.3	137.56	H-Bond (Protein Donor)	false
O7A	NH2	ARG- 364	3.16	137.6	H-Bond (Protein Donor)	false
O7A	NE	ARG- 364	3.07	142.29	H-Bond (Protein Donor)	false
O7A	CZ	ARG- 364	3.53	0	Ionic (Protein Cationic)	false
C1B	CD1	LEU- 366	4.14	0	Hydrophobic	false
O5P	ND2	ASN- 369	3.01	163.64	H-Bond (Protein Donor)	false
C1	CB	ASN- 369	4.41	0	Hydrophobic	false
C1	CG1	VAL- 370	4.42	0	Hydrophobic	false
O1A	NE	ARG- 414	3.22	155.26	H-Bond (Protein Donor)	false
O2A	NE	ARG- 414	3.31	138.61	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 414	3	151.52	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 414	3.59	0	Ionic (Protein Cationic)	false
O5A	CZ	ARG- 414	3.3	0	Ionic (Protein Cationic)	false
CCP	CG2	ILE- 415	4.5	0	Hydrophobic	false
CEP	CG2	ILE- 415	4.1	0	Hydrophobic	false