scPDB - 2ncd entry

Protein Data Bank Entry:

PDB ID : 2ncd

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1999-06-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protein claret segregational
ID:	NCD_DROME
AC:	P20480
Organism:	Drosophila melanogaster
Reign:	Eukaryota
TaxID:	7227
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	13.292
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.182	256.500

% Hydrophobic	% Polar
64.47	35.53
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	51.74 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
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
6.19448	53.4542	43.9998

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
C1'	CD2	LEU- 359	3.82	0	Hydrophobic	false
O1B	N	GLY- 437	2.6	153.75	H-Bond (Protein Donor)	false
O2B	OG	SER- 438	3.21	153.43	H-Bond (Protein Donor)	false
O2B	N	SER- 438	2.76	128.92	H-Bond (Protein Donor)	false
O2B	N	GLY- 439	3.34	162.8	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 440	3.68	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 440	2.95	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 440	2.95	128.65	H-Bond (Protein Donor)	false
O2A	N	TYR- 442	3	169.54	H-Bond (Protein Donor)	false
C5'	CB	TYR- 442	3.67	0	Hydrophobic	false
C2'	CD2	TYR- 442	3.7	0	Hydrophobic	false
DuAr	DuAr	TYR- 442	3.75	0	Aromatic Face/Face	false