scPDB - 3okf entry

Protein Data Bank Entry:

PDB ID : 3okf

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2010-08-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-dehydroquinate synthase
ID:	AROB_VIBCH
AC:	Q9KNV2
Organism:	Vibrio cholerae serotype O1
Reign:	Bacteria
TaxID:	243277
EC Number:	4.2.3.4

Chains:

Chain Name:	Percentage of Residues within binding site
A	2 %
B	98 %

Ligand binding site composition:

B-Factor:	46.330
Number of residues:	49
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.650	1744.875

% Hydrophobic	% Polar
38.88	61.12
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	62 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-62.37	-29.3449	-12.3272

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
O2B	ND2	ASN- 46	3.25	136.7	H-Bond (Protein Donor)	false
O3B	OD2	ASP- 75	2.92	146.79	H-Bond (Ligand Donor)	false
O3B	OD1	ASP- 75	2.98	148.22	H-Bond (Ligand Donor)	false
O3D	OE1	GLU- 77	2.63	150.89	H-Bond (Ligand Donor)	false
O3D	NZ	LYS- 80	2.81	167.25	H-Bond (Protein Donor)	false
O1N	N	GLY- 109	2.81	174.74	H-Bond (Protein Donor)	false
O1A	N	VAL- 110	3	172.1	H-Bond (Protein Donor)	false
C4D	CG2	VAL- 110	4.04	0	Hydrophobic	false
N7N	OD1	ASP- 113	2.58	146.74	H-Bond (Ligand Donor)	false
N7A	OG1	THR- 133	2.96	172.51	H-Bond (Protein Donor)	false
N6A	O	THR- 133	3.16	133.64	H-Bond (Ligand Donor)	false
C5B	CG2	THR- 134	4.21	0	Hydrophobic	false
O1N	OG1	THR- 134	2.71	154.92	H-Bond (Protein Donor)	false
C5N	CD2	LEU- 136	3.52	0	Hydrophobic	false
C4N	CB	ASP- 140	3.55	0	Hydrophobic	false
N7N	O	LYS- 146	2.87	143.33	H-Bond (Ligand Donor)	false
O2D	ND2	ASN- 156	3.1	155.16	H-Bond (Protein Donor)	false
N6A	O	CYS- 173	3.04	141.41	H-Bond (Ligand Donor)	false
N6A	OG1	THR- 176	3.5	126.21	H-Bond (Ligand Donor)	false
N1A	OG1	THR- 176	2.7	147.43	H-Bond (Protein Donor)	false
C5B	CG	GLU- 181	4.47	0	Hydrophobic	false
O7N	O	HOH- 409	2.76	164.2	H-Bond (Protein Donor)	false