scPDB - 1kph entry

Protein Data Bank Entry:

PDB ID : 1kph

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2001-12-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cyclopropane mycolic acid synthase 1
ID:	CMAS1_MYCTU
AC:	P9WPB7
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	2.1.1.79

Chains:

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

Ligand binding site composition:

B-Factor:	13.396
Number of residues:	39
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.233	330.750

% Hydrophobic	% Polar
61.22	38.78
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	77.59 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
11.8168	79.1393	96.6905

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
C2'	CG1	VAL- 12	3.73	0	Hydrophobic	false
SD	CE2	TYR- 16	3.38	0	Hydrophobic	false
C5'	CZ	TYR- 16	3.56	0	Hydrophobic	false
C3'	CE1	TYR- 16	4.17	0	Hydrophobic	false
OXT	N	TYR- 33	2.83	172.09	H-Bond (Protein Donor)	false
O	OG	SER- 34	2.66	174.98	H-Bond (Protein Donor)	false
N	O	GLY- 72	2.81	169.01	H-Bond (Ligand Donor)	false
O3'	N	GLY- 74	3.13	131.87	H-Bond (Protein Donor)	false
O2'	OG1	THR- 94	2.85	144.67	H-Bond (Ligand Donor)	false
O2'	N	LEU- 95	3.15	157.89	H-Bond (Protein Donor)	false
O3'	OE1	GLN- 99	2.64	166.2	H-Bond (Ligand Donor)	false
N1	N	TRP- 123	3.27	144.59	H-Bond (Protein Donor)	false
N6	OE2	GLU- 124	3.06	164.68	H-Bond (Ligand Donor)	false
N6	OE1	GLU- 124	3.33	122.32	H-Bond (Ligand Donor)	false
N	O	ILE- 136	2.79	159.77	H-Bond (Ligand Donor)	false
C4'	CB	ALA- 138	4.28	0	Hydrophobic	false
C1'	CB	ALA- 138	4.17	0	Hydrophobic	false
OXT	O	HOH- 1010	2.7	162.36	H-Bond (Protein Donor)	false
N	O	HOH- 1039	2.87	141.56	H-Bond (Ligand Donor)	false