scPDB - 1xdi entry

Protein Data Bank Entry:

PDB ID : 1xdi

Resolution :2.810 Å

Experimental Method : X-ray

Deposition Date : 2004-09-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD(P)H dehydrogenase (quinone)
ID:	LPDA_MYCTU
AC:	P9WHH7
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	5 %
B	95 %

Ligand binding site composition:

B-Factor:	8.541
Number of residues:	65
Including
Standard Amino Acids:	63
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.343	1258.875

% Hydrophobic	% Polar
43.43	56.57
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	72.68 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
4.88796	39.5477	-31.3111

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
O1P	N	ALA- 13	2.86	162.58	H-Bond (Protein Donor)	false
O2B	OD2	ASP- 35	2.73	158.53	H-Bond (Ligand Donor)	false
N3A	N	CYS- 36	3.05	144.85	H-Bond (Protein Donor)	false
C1B	SG	CYS- 36	4.15	0	Hydrophobic	false
C2B	CB	ASP- 37	4.05	0	Hydrophobic	false
O2B	N	ASP- 37	2.88	145.04	H-Bond (Protein Donor)	false
O3B	N	ALA- 42	2.92	131.68	H-Bond (Protein Donor)	false
O2A	N	ALA- 43	3.26	161.88	H-Bond (Protein Donor)	false
C4'	CB	ALA- 43	4.26	0	Hydrophobic	false
C7	CB	ASP- 47	3.83	0	Hydrophobic	false
C8	CB	ASP- 47	3.46	0	Hydrophobic	false
C6	CB	CYS- 48	4.35	0	Hydrophobic	false
C9A	CB	CYS- 48	3.9	0	Hydrophobic	false
C7M	CB	SER- 51	4.5	0	Hydrophobic	false
N5	NZ	LYS- 52	3.13	161.93	H-Bond (Protein Donor)	false
N6A	O	GLY- 117	3.46	169.38	H-Bond (Ligand Donor)	false
N1A	N	GLY- 117	2.99	154.7	H-Bond (Protein Donor)	false
C7M	CD2	TRP- 172	4.21	0	Hydrophobic	false
C8M	CE2	TRP- 172	3.37	0	Hydrophobic	false
C7M	CB	THR- 193	4.13	0	Hydrophobic	false
C6	CG2	THR- 193	3.8	0	Hydrophobic	false
C7M	CE2	PHE- 197	4.16	0	Hydrophobic	false
O3'	OD2	ASP- 317	3.39	120.63	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 317	3.05	172.99	H-Bond (Ligand Donor)	false
C5'	CB	ASP- 317	4.05	0	Hydrophobic	false
O2P	N	ASP- 317	3.05	143.13	H-Bond (Protein Donor)	false
N1	N	ALA- 325	2.98	162.97	H-Bond (Protein Donor)	false
O2	N	ALA- 325	2.76	121.4	H-Bond (Protein Donor)	false
C4'	CB	ALA- 325	4.02	0	Hydrophobic	false
O2	N	SER- 326	3.48	152.36	H-Bond (Protein Donor)	false
C5'	CB	ALA- 328	4.15	0	Hydrophobic	false
N3	O	TYR- 450	2.58	139.47	H-Bond (Ligand Donor)	false
O1P	O	HOH- 1024	2.98	161.86	H-Bond (Protein Donor)	false