scPDB - 5ayz entry

Protein Data Bank Entry:

PDB ID : 5ayz

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2015-09-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Nicotinate-nucleotide pyrophosphorylase [carboxylating]
ID:	NADC_HUMAN
AC:	Q15274
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.4.2.19

Chains:

Chain Name:	Percentage of Residues within binding site
K	93 %
L	7 %

Ligand binding site composition:

B-Factor:	31.363
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.175	918.000

% Hydrophobic	% Polar
31.62	68.38
According to VolSite

Ligand :

HET Code:	NCN
Formula:	C11H12NO9P
Molecular weight:	333.188 g/mol
DrugBank ID:	DB02382
Buried Surface Area:	68 %
Polar Surface area:	175.93 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	2
Rings:	2
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
-13.2443	1.10477	-25.3667

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
C5	CG2	THR- 137	3.99	0	Hydrophobic	false
C4	CB	THR- 137	4.44	0	Hydrophobic	false
O7	NH1	ARG- 138	3.02	152.22	H-Bond (Protein Donor)	false
O3P	NZ	LYS- 139	3.64	0	Ionic (Protein Cationic)	false
O5'	NZ	LYS- 139	3.25	145.69	H-Bond (Protein Donor)	false
O7	CZ	ARG- 161	3.68	0	Ionic (Protein Cationic)	false
O8	CZ	ARG- 161	3.71	0	Ionic (Protein Cationic)	false
O7	NH2	ARG- 161	2.93	167.64	H-Bond (Protein Donor)	false
O8	NE	ARG- 161	2.82	165.56	H-Bond (Protein Donor)	false
C3	SD	MET- 169	3.83	0	Hydrophobic	false
O7	NZ	LYS- 171	2.95	160.55	H-Bond (Protein Donor)	false
O7	NZ	LYS- 171	2.95	0	Ionic (Protein Cationic)	false
C2'	CD1	LEU- 220	4.07	0	Hydrophobic	false
C5	CD1	LEU- 220	4.29	0	Hydrophobic	false
O3'	OD1	ASP- 222	3.05	145.3	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 222	3.2	150.33	H-Bond (Ligand Donor)	false
C5'	CB	SER- 248	4.49	0	Hydrophobic	false
C2'	CB	SER- 248	4.03	0	Hydrophobic	false
O1P	N	GLY- 250	2.97	170.95	H-Bond (Protein Donor)	false
C5	CB	SER- 268	4.14	0	Hydrophobic	false
O2P	N	GLY- 270	3.08	155.01	H-Bond (Protein Donor)	false
O2P	O	HOH- 506	2.82	164.15	H-Bond (Protein Donor)	false