scPDB - 1yl7 entry

Protein Data Bank Entry:

PDB ID : 1yl7

Resolution :2.340 Å

Experimental Method : X-ray

Deposition Date : 2005-01-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	4-hydroxy-tetrahydrodipicolinate reductase
ID:	DAPB_MYCTU
AC:	P9WP23
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	40.338
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.304	270.000

% Hydrophobic	% Polar
47.50	52.50
According to VolSite

Ligand :

HET Code:	NAI
Formula:	C21H27N7O14P2
Molecular weight:	663.425 g/mol
DrugBank ID:	DB00157
Buried Surface Area:	59.12 %
Polar Surface area:	342.9 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	6
Rings:	5
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
110.674	-13.6193	16.0217

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
O1A	N	LYS- 11	3.03	162.22	H-Bond (Protein Donor)	false
O1N	NZ	LYS- 11	3.69	0	Ionic (Protein Cationic)	false
O2N	N	VAL- 12	2.77	169.68	H-Bond (Protein Donor)	false
O3B	OD1	ASP- 33	3.12	156.15	H-Bond (Ligand Donor)	false
O3B	OD2	ASP- 33	2.69	135.03	H-Bond (Ligand Donor)	false
C5D	CB	PHE- 52	4.22	0	Hydrophobic	false
C1D	CD2	PHE- 52	4.39	0	Hydrophobic	false
C4N	CE2	PHE- 52	4.17	0	Hydrophobic	false
N7N	O	GLY- 75	3.15	152.09	H-Bond (Ligand Donor)	false
C4D	CG2	THR- 76	4.3	0	Hydrophobic	false
O3D	N	THR- 77	3.38	175.68	H-Bond (Protein Donor)	false
O2D	OG1	THR- 77	2.79	154.21	H-Bond (Ligand Donor)	false
C1D	CG2	THR- 77	4.09	0	Hydrophobic	false
N7N	O	ALA- 102	2.98	123.1	H-Bond (Ligand Donor)	false
O7N	N	PHE- 105	2.62	163.22	H-Bond (Protein Donor)	false
C4N	CZ	PHE- 217	3.55	0	Hydrophobic	false
O2N	O	HOH- 503	2.6	179.96	H-Bond (Protein Donor)	false