scPDB - 4h2i entry

Protein Data Bank Entry:

PDB ID : 4h2i

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2012-09-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	5'-nucleotidase
ID:	5NTD_HUMAN
AC:	P21589
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.1.3.5

Chains:

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

Ligand binding site composition:

B-Factor:	31.288
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	ZN ZN

Cavity properties

Ligandability	Volume (Å3)
0.534	1906.875

% Hydrophobic	% Polar
40.18	59.82
According to VolSite

Ligand :

HET Code:	A12
Formula:	C11H14N5O9P2
Molecular weight:	422.204 g/mol
DrugBank ID:	-
Buried Surface Area:	64.99 %
Polar Surface area:	251.48 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-15.7606	19.5879	-33.212

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	ND2	ASN- 117	2.58	149.89	H-Bond (Protein Donor)	false
O2B	NE2	HIS- 118	2.6	172.41	H-Bond (Protein Donor)	false
O1A	ND2	ASN- 245	3.05	159.91	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 354	3.73	0	Ionic (Protein Cationic)	false
O2A	NH1	ARG- 354	2.86	158.99	H-Bond (Protein Donor)	false
O5'	NH2	ARG- 354	3.25	153.62	H-Bond (Protein Donor)	false
O2'	ND2	ASN- 390	3.05	169.69	H-Bond (Protein Donor)	false
N3	ND2	ASN- 390	3.16	138.39	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 395	3.94	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 395	3.87	0	Ionic (Protein Cationic)	false
O1B	NH1	ARG- 395	3.01	171.98	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 395	3.31	139.95	H-Bond (Protein Donor)	false
O5'	NH2	ARG- 395	2.95	140.96	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 417	3.98	0	Aromatic Face/Face	false
C2'	CZ	PHE- 500	3.94	0	Hydrophobic	false
DuAr	DuAr	PHE- 500	3.8	0	Aromatic Face/Face	false
O3'	OD1	ASP- 506	2.55	155.17	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 506	3.35	127.81	H-Bond (Ligand Donor)	false
O1B	ZN	ZN- 601	2.06	0	Metal Acceptor	false
O3B	ZN	ZN- 602	2.09	0	Metal Acceptor	false