scPDB - 5cts entry

Protein Data Bank Entry:

PDB ID : 5cts

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 1989-11-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Citrate synthase, mitochondrial
ID:	CISY_CHICK
AC:	P23007
Organism:	Gallus gallus
Reign:	Eukaryota
TaxID:	9031
EC Number:	2.3.3.1

Chains:

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

Ligand binding site composition:

B-Factor:	12.948
Number of residues:	42
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.182	1512.000

% Hydrophobic	% Polar
40.85	59.15
According to VolSite

Ligand :

HET Code:	CMC
Formula:	C23H33N7O18P3S
Molecular weight:	820.530 g/mol
DrugBank ID:	-
Buried Surface Area:	53.99 %
Polar Surface area:	452.74 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	21

Mass center Coordinates

X	Y	Z
15.6918	-9.7549	9.9654

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
O4A	NE	ARG- 46	2.82	146.75	H-Bond (Protein Donor)	false
O4A	NH1	ARG- 46	3.31	125.23	H-Bond (Protein Donor)	false
O5A	NH1	ARG- 46	2.84	165.79	H-Bond (Protein Donor)	false
O4A	CZ	ARG- 46	3.44	0	Ionic (Protein Cationic)	false
O5A	CZ	ARG- 46	3.8	0	Ionic (Protein Cationic)	false
CEP	CB	LEU- 273	4.21	0	Hydrophobic	false
C6P	CD2	LEU- 273	4.18	0	Hydrophobic	false
N4P	O	LEU- 273	3.07	142.91	H-Bond (Ligand Donor)	false
O21	ND1	HIS- 274	2.8	148.36	H-Bond (Protein Donor)	false
C6P	CG2	VAL- 314	4.19	0	Hydrophobic	false
N1A	N	VAL- 315	2.99	156.03	H-Bond (Protein Donor)	false
N6A	O	VAL- 315	2.6	139.08	H-Bond (Ligand Donor)	false
O5P	N	GLY- 317	2.6	149.64	H-Bond (Protein Donor)	false
N6A	O	TYR- 318	2.89	149.76	H-Bond (Ligand Donor)	false
N8P	O	TYR- 318	3.04	133.2	H-Bond (Ligand Donor)	false
CCP	CB	ALA- 321	4.46	0	Hydrophobic	false
C1B	CB	ALA- 366	4.4	0	Hydrophobic	false
C4B	CB	ALA- 366	3.93	0	Hydrophobic	false
O1A	N	ALA- 368	2.64	170.04	H-Bond (Protein Donor)	false
O5P	ND2	ASN- 373	3.41	166.44	H-Bond (Protein Donor)	false
S1P	CB	ASN- 373	3.65	0	Hydrophobic	false
C1	CG1	VAL- 374	3.75	0	Hydrophobic	false
O22	OD1	ASP- 375	2.58	143.6	H-Bond (Protein Donor)	false
O1A	O	HOH- 539	2.6	158.68	H-Bond (Protein Donor)	false