scPDB - 4ha9 entry

Protein Data Bank Entry:

PDB ID : 4ha9

Resolution :2.350 Å

Experimental Method : X-ray

Deposition Date : 2012-09-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase
ID:	RIB7_YEAST
AC:	P33312
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	1.1.1.302

Chains:

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

Ligand binding site composition:

B-Factor:	54.465
Number of residues:	40
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.501	286.875

% Hydrophobic	% Polar
37.65	62.35
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	57.88 %
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
-24.9968	0.614854	-12.5458

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
C4N	CB	TYR- 36	3.54	0	Hydrophobic	false
O7N	N	ALA- 37	2.7	152.13	H-Bond (Protein Donor)	false
C3N	CB	VAL- 44	3.56	0	Hydrophobic	false
C4D	CG2	VAL- 44	4.41	0	Hydrophobic	false
C4N	CG1	VAL- 44	3.82	0	Hydrophobic	false
O2B	OG	SER- 77	3.46	147.59	H-Bond (Protein Donor)	false
O1A	N	THR- 79	3.25	142.81	H-Bond (Protein Donor)	false
O1A	OG1	THR- 79	2.76	161.94	H-Bond (Protein Donor)	false
C2D	CB	THR- 79	3.84	0	Hydrophobic	false
C1B	CG2	ILE- 105	4.17	0	Hydrophobic	false
O3X	OG1	THR- 107	3.06	131.59	H-Bond (Protein Donor)	false
N6A	O	VAL- 159	3.45	148.01	H-Bond (Ligand Donor)	false
N1A	N	VAL- 159	2.85	168.38	H-Bond (Protein Donor)	false
O5D	N	ALA- 183	3.29	133.49	H-Bond (Protein Donor)	false
C5D	CB	ALA- 183	4.08	0	Hydrophobic	false
C5B	CB	ASN- 184	3.79	0	Hydrophobic	false
O1N	N	ASN- 184	2.7	147.87	H-Bond (Protein Donor)	false
O2A	N	VAL- 185	3.02	141.52	H-Bond (Protein Donor)	false
C5N	CD1	ILE- 186	3.63	0	Hydrophobic	false
N7A	NE2	GLN- 188	2.99	153.19	H-Bond (Protein Donor)	false
N6A	OE1	GLN- 188	3.2	136.66	H-Bond (Ligand Donor)	false