scPDB - 3i99 entry

Protein Data Bank Entry:

PDB ID : 3i99

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2009-07-10

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_VIBCH
AC:	Q9KV40
Organism:	Vibrio cholerae serotype O1
Reign:	Bacteria
TaxID:	243277
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	24.383
Number of residues:	59
Including
Standard Amino Acids:	55
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.363	2187.000

% Hydrophobic	% Polar
43.67	56.33
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	72.72 %
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
37.2698	11.5059	21.7352

Binding mode :

What is Poseview ?

2D View
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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
C8M	CB	THR- 24	4.13	0	Hydrophobic	false
O2B	O	ILE- 59	2.57	153.73	H-Bond (Ligand Donor)	false
C1B	CG2	ILE- 59	4.31	0	Hydrophobic	false
O2A	N	GLY- 61	2.81	139.08	H-Bond (Protein Donor)	false
O1P	N	LYS- 62	3.02	161.28	H-Bond (Protein Donor)	false
O2P	N	LYS- 62	3.35	121.38	H-Bond (Protein Donor)	false
O2A	N	GLY- 63	2.93	135.06	H-Bond (Protein Donor)	false
C8M	CB	SER- 64	3.94	0	Hydrophobic	false
C9	CB	SER- 64	4.31	0	Hydrophobic	false
C2'	CB	SER- 64	4.45	0	Hydrophobic	false
O2'	OG	SER- 64	3.28	152.47	H-Bond (Ligand Donor)	false
O2P	N	SER- 64	2.71	165.71	H-Bond (Protein Donor)	false
O2P	OG	SER- 64	2.71	153.93	H-Bond (Protein Donor)	false
O1A	N	ASN- 65	2.83	146.33	H-Bond (Protein Donor)	false
C5B	CB	ASN- 65	4.23	0	Hydrophobic	false
C5'	CB	ASN- 65	3.87	0	Hydrophobic	false
C2'	CB	ASN- 65	4.1	0	Hydrophobic	false
C3B	CE	MET- 66	3.38	0	Hydrophobic	false
C2'	CG2	ILE- 124	4.39	0	Hydrophobic	false
C7	CG	PRO- 125	3.71	0	Hydrophobic	false
C8	CG	PRO- 125	3.7	0	Hydrophobic	false
O1P	N	CYS- 127	3	162.22	H-Bond (Protein Donor)	false
C5'	CB	SER- 130	4.15	0	Hydrophobic	false
O1P	OG	SER- 130	2.8	166.93	H-Bond (Protein Donor)	false
C4B	CG2	ILE- 133	4.48	0	Hydrophobic	false
C1B	CG2	ILE- 133	4.37	0	Hydrophobic	false
C3'	CG2	ILE- 136	3.87	0	Hydrophobic	false
O2	N	GLY- 137	3.29	154.42	H-Bond (Protein Donor)	false
N3	O	GLY- 137	2.82	176.5	H-Bond (Ligand Donor)	false
N6A	O	VAL- 187	3.11	167	H-Bond (Ligand Donor)	false
N1A	N	VAL- 187	2.76	175.86	H-Bond (Protein Donor)	false
O4	NH1	ARG- 227	3.05	169.51	H-Bond (Protein Donor)	false
N5	NH2	ARG- 227	3.03	156.01	H-Bond (Protein Donor)	false
C6	CD2	LEU- 231	4.06	0	Hydrophobic	false
C7M	CG	PRO- 234	4.13	0	Hydrophobic	false
C8M	CG	PRO- 234	4.3	0	Hydrophobic	false
C3B	CG	ARG- 339	4.2	0	Hydrophobic	false