scPDB - 3ngl entry

Protein Data Bank Entry:

PDB ID : 3ngl

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2010-06-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Bifunctional protein FolD
ID:	FOLD_THEAC
AC:	Q05213
Organism:	Thermoplasma acidophilum
Reign:	Archaea
TaxID:	273075
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	97 %
C	3 %

Ligand binding site composition:

B-Factor:	22.422
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.364	992.250

% Hydrophobic	% Polar
50.68	49.32
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	51.11 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
3.08425	-12.3169	20.2301

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
C4N	CB	THR- 135	4.12	0	Hydrophobic	false
C4B	CB	ASN- 157	4.31	0	Hydrophobic	false
O2N	ND2	ASN- 157	2.66	160.17	H-Bond (Protein Donor)	false
O3B	N	ARG- 158	3.07	153.54	H-Bond (Protein Donor)	false
O1X	NH2	ARG- 158	3.47	126.66	H-Bond (Protein Donor)	false
O1X	NE	ARG- 158	2.66	168.69	H-Bond (Protein Donor)	false
O2X	NH2	ARG- 158	2.6	145.63	H-Bond (Protein Donor)	false
O2X	NE	ARG- 158	3.36	124.47	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 158	3.5	0	Ionic (Protein Cationic)	false
O2X	CZ	ARG- 158	3.39	0	Ionic (Protein Cationic)	false
O2N	OG	SER- 159	2.67	153.83	H-Bond (Protein Donor)	false
C5N	CG2	VAL- 161	4	0	Hydrophobic	false
C5N	CG2	VAL- 162	4.16	0	Hydrophobic	false
O2B	N	SER- 182	3.46	142.76	H-Bond (Protein Donor)	false
O2X	N	SER- 182	3.4	147.61	H-Bond (Protein Donor)	false
O2X	OG	SER- 182	2.75	164.79	H-Bond (Protein Donor)	false
C4D	CB	ALA- 200	4.16	0	Hydrophobic	false
C1B	CG1	VAL- 201	4.08	0	Hydrophobic	false
C3N	CG1	VAL- 221	4.49	0	Hydrophobic	false
O3D	N	ILE- 223	3	168.66	H-Bond (Protein Donor)	false
C3N	CD1	ILE- 223	3.7	0	Hydrophobic	false