scPDB - 3h2s entry

Protein Data Bank Entry:

PDB ID : 3h2s

Resolution :1.780 Å

Experimental Method : X-ray

Deposition Date : 2009-04-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative NADH-flavin reductase
ID:	Q03B84_LACC3
AC:	Q03B84
Organism:	Lactobacillus casei
Reign:	Bacteria
TaxID:	321967
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	14.536
Number of residues:	48
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.785	671.625

% Hydrophobic	% Polar
41.71	58.29
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	56.68 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
20.7009	46.0531	9.23269

Binding mode :

What is Poseview ?

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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
O3B	OG1	THR- 9	3.09	160.5	H-Bond (Ligand Donor)	false
O1X	OG1	THR- 9	2.57	148.45	H-Bond (Protein Donor)	false
O2A	N	ARG- 11	2.78	165.15	H-Bond (Protein Donor)	false
O2N	NH1	ARG- 11	2.82	146.77	H-Bond (Protein Donor)	false
O2N	CZ	ARG- 11	3.94	0	Ionic (Protein Cationic)	false
O1N	N	ALA- 12	2.71	163.81	H-Bond (Protein Donor)	false
C5D	CB	ALA- 12	3.9	0	Hydrophobic	false
O2B	NE	ARG- 32	3.49	124.66	H-Bond (Protein Donor)	false
O2X	NE	ARG- 32	2.98	170.52	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 32	2.86	175.08	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 32	3.88	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 32	3.73	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 32	3.96	159.68	Pi/Cation	false
C1B	CD2	LEU- 70	3.63	0	Hydrophobic	false
C5B	CB	SER- 71	3.77	0	Hydrophobic	false
C5D	CB	SER- 71	4.32	0	Hydrophobic	false
C3D	CB	SER- 71	3.69	0	Hydrophobic	false
O4B	N	SER- 71	3.35	157.32	H-Bond (Protein Donor)	false
O2D	OG	SER- 71	3.34	138.33	H-Bond (Protein Donor)	false
C5D	CD1	ILE- 103	4.49	0	Hydrophobic	false
C4D	CG2	ILE- 103	3.71	0	Hydrophobic	false
O7N	N	SER- 106	2.55	150.35	H-Bond (Protein Donor)	false
N7N	OG	SER- 106	2.78	152.07	H-Bond (Ligand Donor)	false
O3D	NE2	GLN- 138	3.15	129.89	H-Bond (Protein Donor)	false
O2D	OE1	GLN- 138	2.65	134.61	H-Bond (Ligand Donor)	false
C3N	CG	PRO- 158	4.13	0	Hydrophobic	false
N7N	O	GLU- 160	3.18	126.23	H-Bond (Ligand Donor)	false
C5D	CE2	PHE- 162	4.34	0	Hydrophobic	false
C5N	CB	PHE- 162	3.65	0	Hydrophobic	false
O1N	O	HOH- 414	2.62	169.69	H-Bond (Protein Donor)	false
O2X	O	HOH- 447	2.72	179.94	H-Bond (Protein Donor)	false