scPDB - 2iyp entry

Protein Data Bank Entry:

PDB ID : 2iyp

Resolution :2.790 Å

Experimental Method : X-ray

Deposition Date : 2006-07-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	6-phosphogluconate dehydrogenase, decarboxylating
ID:	6PGD_LACLM
AC:	P96789
Organism:	Lactococcus lactis subsp. cremoris
Reign:	Bacteria
TaxID:	416870
EC Number:	1.1.1.44

Chains:

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

Ligand binding site composition:

B-Factor:	40.766
Number of residues:	19
Including
Standard Amino Acids:	19
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.180	334.125

% Hydrophobic	% Polar
46.46	53.54
According to VolSite

Ligand :

HET Code:	A2P
Formula:	C10H11N5O10P2
Molecular weight:	423.169 g/mol
DrugBank ID:	DB02098
Buried Surface Area:	47.5 %
Polar Surface area:	263.53 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
25.4254	19.1481	92.9357

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
O3'	N	MET- 11	3.4	121.21	H-Bond (Protein Donor)	false
C3'	CB	ALA- 12	4.1	0	Hydrophobic	false
O1P	ND2	ASN- 33	2.73	158.67	H-Bond (Protein Donor)	false
O2P	CZ	ARG- 34	3.67	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 34	3.82	0	Ionic (Protein Cationic)	false
O2P	NH2	ARG- 34	2.84	130.93	H-Bond (Protein Donor)	false
O3P	NE	ARG- 34	3.05	139.99	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 34	3.77	170.64	Pi/Cation	false
O1P	NZ	LYS- 38	3.6	0	Ionic (Protein Cationic)	false
C1'	CG1	VAL- 74	3.94	0	Hydrophobic	false
O4'	N	GLN- 75	3.45	136.37	H-Bond (Protein Donor)	false