scPDB - 4pyt entry

Protein Data Bank Entry:

PDB ID : 4pyt

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2014-03-27

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_BACLD
AC:	Q65JX9
Organism:	Bacillus licheniformis
Reign:	Bacteria
TaxID:	279010
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	29.038
Number of residues:	57
Including
Standard Amino Acids:	52
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.115	1312.875

% Hydrophobic	% Polar
38.56	61.44
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	77.5 %
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
24.0522	49.8746	83.3925

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
C8M	CB	THR- 27	4.38	0	Hydrophobic	false
O2B	NH1	ARG- 61	3.07	132.55	H-Bond (Protein Donor)	false
O2B	O	ALA- 62	2.69	151.33	H-Bond (Ligand Donor)	false
O2A	N	GLY- 64	2.8	158.57	H-Bond (Protein Donor)	false
O1P	N	ARG- 65	3.36	159.52	H-Bond (Protein Donor)	false
O2A	N	GLY- 66	2.86	138.29	H-Bond (Protein Donor)	false
C8M	CB	SER- 67	4.24	0	Hydrophobic	false
C9	CB	SER- 67	4.31	0	Hydrophobic	false
C2'	CB	SER- 67	4.05	0	Hydrophobic	false
O2'	OG	SER- 67	2.76	143.53	H-Bond (Ligand Donor)	false
O2P	N	SER- 67	2.95	152.51	H-Bond (Protein Donor)	false
O1A	N	ASN- 68	2.81	157.28	H-Bond (Protein Donor)	false
C1'	CB	ASN- 68	4.13	0	Hydrophobic	false
C5B	CD2	LEU- 69	4.08	0	Hydrophobic	false
C3B	CD2	LEU- 69	4.02	0	Hydrophobic	false
C3'	CG2	ILE- 126	4.13	0	Hydrophobic	false
C8	CG	PRO- 127	3.49	0	Hydrophobic	false
O1P	OG	SER- 129	2.61	167.26	H-Bond (Protein Donor)	false
O1P	N	SER- 129	2.87	161.6	H-Bond (Protein Donor)	false
C4B	CD2	TYR- 135	3.63	0	Hydrophobic	false
C3B	CE2	TYR- 135	4.21	0	Hydrophobic	false
C1B	CD2	TYR- 135	3.76	0	Hydrophobic	false
C4B	SD	MET- 136	4.41	0	Hydrophobic	false
O2	N	GLY- 139	2.97	158.65	H-Bond (Protein Donor)	false
N3	O	GLY- 139	2.68	173.07	H-Bond (Ligand Donor)	false
N6A	O	CYS- 186	3.01	159.14	H-Bond (Ligand Donor)	false
N1A	N	CYS- 186	2.87	161.03	H-Bond (Protein Donor)	false
O4	NH1	ARG- 212	3.32	125.06	H-Bond (Protein Donor)	false
O4	NH2	ARG- 212	2.62	155.24	H-Bond (Protein Donor)	false
N5	NH1	ARG- 212	2.93	146.44	H-Bond (Protein Donor)	false
C7M	SG	CYS- 222	3.66	0	Hydrophobic	false
C8M	SG	CYS- 222	4.28	0	Hydrophobic	false
C7M	CE2	PHE- 261	4.04	0	Hydrophobic	false
O3B	OE2	GLU- 297	3.21	140.45	H-Bond (Ligand Donor)	false
O3B	OE1	GLU- 297	2.69	156.07	H-Bond (Ligand Donor)	false