scPDB - 4cdg entry

Protein Data Bank Entry:

PDB ID : 4cdg

Resolution :2.790 Å

Experimental Method : X-ray

Deposition Date : 2013-10-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Bloom syndrome protein
ID:	BLM_HUMAN
AC:	P54132
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.6.4.12

Chains:

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

Ligand binding site composition:

B-Factor:	55.412
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.527	1869.750

% Hydrophobic	% Polar
40.25	59.75
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	58.69 %
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
15.3213	130.554	-42.7499

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
N6	O	ASN- 667	3.04	148.98	H-Bond (Ligand Donor)	false
O4'	NH1	ARG- 669	3.25	124.09	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 669	3.82	28.61	Pi/Cation	false
N7	NE2	GLN- 672	3.41	164.46	H-Bond (Protein Donor)	false
N6	OE1	GLN- 672	3.02	131.38	H-Bond (Ligand Donor)	false
O1B	N	GLY- 692	2.89	153.23	H-Bond (Protein Donor)	false
O2B	N	GLY- 694	3.43	172.03	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 695	2.83	148.94	H-Bond (Protein Donor)	false
O2B	N	LYS- 695	3.22	163.16	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 695	2.83	0	Ionic (Protein Cationic)	false
O3B	OG	SER- 696	3.33	125.76	H-Bond (Protein Donor)	false
O2A	N	SER- 696	3.35	147.49	H-Bond (Protein Donor)	false
O2A	OG	SER- 696	2.71	149.85	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 982	3.47	0	Ionic (Protein Cationic)	false
O3B	CZ	ARG- 982	3.84	0	Ionic (Protein Cationic)	false
O1A	CZ	ARG- 982	3.35	0	Ionic (Protein Cationic)	false
O3B	NH2	ARG- 982	2.99	132.44	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 982	3.14	130.44	H-Bond (Protein Donor)	false
O1A	NE	ARG- 982	2.75	148.35	H-Bond (Protein Donor)	false