scPDB - 3tx1 entry

Protein Data Bank Entry:

PDB ID : 3tx1

Resolution :2.690 Å

Experimental Method : X-ray

Deposition Date : 2011-09-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-N-acetylenolpyruvoylglucosamine reductase
ID:	MURB_LISMO
AC:	Q8Y776
Organism:	Listeria monocytogenes serovar 1/2a
Reign:	Bacteria
TaxID:	169963
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	38.586
Number of residues:	53
Including
Standard Amino Acids:	53
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.577	988.875

% Hydrophobic	% Polar
36.86	63.14
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	74.83 %
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
-21.2803	32.8965	-4.48511

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
C7M	CE2	TYR- 24	4.42	0	Hydrophobic	false
C8M	CE2	TYR- 24	3.36	0	Hydrophobic	false
O2B	O	ILE- 59	2.67	158.45	H-Bond (Ligand Donor)	false
O1A	N	GLY- 61	2.87	123.49	H-Bond (Protein Donor)	false
O1P	N	ASN- 62	3.2	164.2	H-Bond (Protein Donor)	false
O2P	N	ASN- 62	3.45	133.1	H-Bond (Protein Donor)	false
O1A	N	GLY- 63	2.64	144.84	H-Bond (Protein Donor)	false
C8M	CB	SER- 64	4.23	0	Hydrophobic	false
C9	CB	SER- 64	4.32	0	Hydrophobic	false
C2'	CB	SER- 64	4.11	0	Hydrophobic	false
O2'	OG	SER- 64	2.78	139.38	H-Bond (Ligand Donor)	false
O2P	OG	SER- 64	2.92	160.62	H-Bond (Protein Donor)	false
O2P	N	SER- 64	2.71	164.74	H-Bond (Protein Donor)	false
O2A	N	ASN- 65	2.78	148.8	H-Bond (Protein Donor)	false
C5B	CB	ASN- 65	4.32	0	Hydrophobic	false
C5'	CB	ASN- 65	3.94	0	Hydrophobic	false
C2'	CB	ASN- 65	3.84	0	Hydrophobic	false
C3B	CD2	LEU- 66	4.19	0	Hydrophobic	false
C3'	CG2	ILE- 122	4.32	0	Hydrophobic	false
C7	CG	PRO- 123	3.57	0	Hydrophobic	false
C8	CG	PRO- 123	3.65	0	Hydrophobic	false
C8	CG	PRO- 123	3.65	0	Hydrophobic	false
O1P	N	SER- 125	2.79	163.72	H-Bond (Protein Donor)	false
O1P	OG	SER- 125	2.88	144.04	H-Bond (Protein Donor)	false
C1B	CB	HIS- 131	3.86	0	Hydrophobic	false
C4B	SD	MET- 132	4.21	0	Hydrophobic	false
C5'	CG	MET- 132	4.41	0	Hydrophobic	false
O2	N	GLY- 135	2.94	151.13	H-Bond (Protein Donor)	false
N3	O	GLY- 135	2.69	160.59	H-Bond (Ligand Donor)	false
O2	NE	ARG- 170	3.47	125.31	H-Bond (Protein Donor)	false
N6A	O	VAL- 181	3.13	170.96	H-Bond (Ligand Donor)	false
N1A	N	VAL- 181	2.97	157.16	H-Bond (Protein Donor)	false
O4	NH2	ARG- 207	3.45	136.77	H-Bond (Protein Donor)	false
O4	NH1	ARG- 207	2.98	163.72	H-Bond (Protein Donor)	false
N5	NH2	ARG- 207	3.27	142.55	H-Bond (Protein Donor)	false
C7M	CD2	LEU- 213	4.11	0	Hydrophobic	false
C7M	CE2	PHE- 256	3.63	0	Hydrophobic	false
C3B	CG	LYS- 292	4.17	0	Hydrophobic	false