scPDB - 4yp6 entry

Protein Data Bank Entry:

PDB ID : 4yp6

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2015-03-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Nicotinamide-nucleotide adenylyltransferase
ID:	NADM_METTH
AC:	O26253
Organism:	Methanothermobacter thermautotrophicus
Reign:	Archaea
TaxID:	187420
EC Number:	2.7.7.1

Chains:

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

Ligand binding site composition:

B-Factor:	21.661
Number of residues:	50
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.968	438.750

% Hydrophobic	% Polar
45.38	54.62
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	57.57 %
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
19.1599	86.4416	-85.0358

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
C4D	CG2	VAL- 9	3.83	0	Hydrophobic	false
O1A	NZ	LYS- 11	3.85	0	Ionic (Protein Cationic)	false
O2A	N	LYS- 11	2.92	162.49	H-Bond (Protein Donor)	false
C3D	CG	LYS- 11	4.04	0	Hydrophobic	false
O2X	NE2	HIS- 16	2.69	174.79	H-Bond (Protein Donor)	false
O3X	NE2	HIS- 19	2.91	152.1	H-Bond (Protein Donor)	false
O3D	OG	SER- 39	2.68	149.12	H-Bond (Ligand Donor)	false
O2D	OD1	ASP- 80	2.93	172.31	H-Bond (Ligand Donor)	false
O7N	N	ILE- 81	2.78	163.71	H-Bond (Protein Donor)	false
N7N	O	ILE- 81	2.98	147.02	H-Bond (Ligand Donor)	false
N7N	OD1	ASN- 84	2.84	158.72	H-Bond (Ligand Donor)	false
DuAr	DuAr	TRP- 87	3.55	0	Aromatic Face/Face	false
C4N	CB	TRP- 87	4.16	0	Hydrophobic	false
C5N	CD2	LEU- 107	3.78	0	Hydrophobic	false
C5N	CG2	VAL- 108	4.14	0	Hydrophobic	false
C4N	CD1	LEU- 111	4.15	0	Hydrophobic	false
N6A	O	LEU- 124	2.92	153.02	H-Bond (Ligand Donor)	false
O2B	OH	TYR- 126	3.18	149	H-Bond (Protein Donor)	false
N1A	N	TYR- 126	3.12	151.37	H-Bond (Protein Donor)	false
O2X	OH	TYR- 126	2.85	140.4	H-Bond (Protein Donor)	false
DuAr	DuAr	TYR- 126	3.61	0	Aromatic Face/Face	false
O1X	N	GLY- 132	3.21	129.43	H-Bond (Protein Donor)	false
O2X	N	GLY- 132	2.88	163.1	H-Bond (Protein Donor)	false
O1X	O	HOH- 2107	2.54	159.28	H-Bond (Protein Donor)	false
O1X	O	HOH- 2110	2.6	179.95	H-Bond (Protein Donor)	false