scPDB - 3cr7 entry

Protein Data Bank Entry:

PDB ID : 3cr7

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2008-04-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Adenylyl-sulfate kinase
ID:	KAPS_PENCH
AC:	Q12657
Organism:	Penicillium chrysogenum
Reign:	Eukaryota
TaxID:	5076
EC Number:	2.7.1.25

Chains:

Chain Name:	Percentage of Residues within binding site
A	97 %
D	3 %

Ligand binding site composition:

B-Factor:	35.113
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	ADP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.338	2187.000

% Hydrophobic	% Polar
47.22	52.78
According to VolSite

Ligand :

HET Code:	PPS
Formula:	C10H11N5O13P2S
Molecular weight:	503.233 g/mol
DrugBank ID:	DB02902
Buried Surface Area:	63.21 %
Polar Surface area:	315.29 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
24.4312	62.4731	66.1681

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
C3'	CB	SER- 34	3.91	0	Hydrophobic	false
OS2	NH2	ARG- 66	3.47	144.83	H-Bond (Protein Donor)	false
O4P	NE	ARG- 66	2.63	170.38	H-Bond (Protein Donor)	false
O4P	CZ	ARG- 66	3.54	0	Ionic (Protein Cationic)	false
C5'	CE2	PHE- 75	4.02	0	Hydrophobic	false
C4'	CZ	PHE- 75	4.4	0	Hydrophobic	false
C1'	CZ	PHE- 75	3.96	0	Hydrophobic	false
OS3	NE	ARG- 80	3.27	149.15	H-Bond (Protein Donor)	false
OS3	NH2	ARG- 80	3.21	150.34	H-Bond (Protein Donor)	false
OS3	CZ	ARG- 80	3.69	0	Ionic (Protein Cationic)	false
OS2	ND2	ASN- 83	3.1	150.18	H-Bond (Protein Donor)	false
O4P	ND2	ASN- 83	3.24	130.75	H-Bond (Protein Donor)	false
O5P	N	ILE- 106	2.77	159.84	H-Bond (Protein Donor)	false
C5'	CD1	ILE- 106	3.51	0	Hydrophobic	false
C3'	CD1	ILE- 106	4.38	0	Hydrophobic	false
OS1	N	SER- 107	2.84	160.84	H-Bond (Protein Donor)	false
O2P	NZ	LYS- 151	2.52	169.92	H-Bond (Protein Donor)	false
O2P	NZ	LYS- 151	2.52	0	Ionic (Protein Cationic)	false
C2'	CD2	LEU- 153	3.46	0	Hydrophobic	false
N6	O	LYS- 163	3.12	124.64	H-Bond (Ligand Donor)	false
N6	O	GLU- 164	3.2	148.35	H-Bond (Ligand Donor)	false
N1	N	THR- 166	3.44	154.85	H-Bond (Protein Donor)	false