scPDB - 4b4o entry

Protein Data Bank Entry:

PDB ID : 4b4o

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2012-07-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Epimerase family protein SDR39U1
ID:	D39U1_HUMAN
AC:	Q9NRG7
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	20.295
Number of residues:	44
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.420	1464.750

% Hydrophobic	% Polar
58.99	41.01
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	57.75 %
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
38.9941	-55.4757	-42.0205

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
O3B	OG1	THR- 9	2.71	146.82	H-Bond (Ligand Donor)	false
O3X	OG1	THR- 9	2.55	156.4	H-Bond (Protein Donor)	false
O2A	N	PHE- 11	2.77	164.3	H-Bond (Protein Donor)	false
O1N	N	ILE- 12	2.79	167.84	H-Bond (Protein Donor)	false
C3N	CD1	ILE- 12	4.16	0	Hydrophobic	false
C5D	CD1	ILE- 12	3.72	0	Hydrophobic	false
O3X	OG	SER- 31	2.55	156.73	H-Bond (Protein Donor)	false
O1X	N	ARG- 32	3.01	164.03	H-Bond (Protein Donor)	false
O1X	NE	ARG- 32	2.79	170.15	H-Bond (Protein Donor)	false
O2X	NH2	ARG- 32	2.98	157.9	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 32	3.6	0	Ionic (Protein Cationic)	false
O2X	CZ	ARG- 32	3.87	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 32	3.72	156.22	Pi/Cation	false
C5D	CB	LEU- 58	4.04	0	Hydrophobic	false
O4B	N	GLY- 60	3.34	160.49	H-Bond (Protein Donor)	false
N6A	OE1	GLU- 61	3.14	174.61	H-Bond (Ligand Donor)	false
O1A	ND2	ASN- 62	3.44	153.27	H-Bond (Protein Donor)	false
O2D	NE	ARG- 82	3.4	139.08	H-Bond (Protein Donor)	false
O2D	NH2	ARG- 82	2.92	161.38	H-Bond (Protein Donor)	false
C2D	CH2	TRP- 139	4.24	0	Hydrophobic	false
C5N	CB	SER- 157	3.46	0	Hydrophobic	false
O7N	N	VAL- 160	3.26	160.73	H-Bond (Protein Donor)	false
C3N	CG2	VAL- 160	3.69	0	Hydrophobic	false
O5B	O	HOH- 2001	3.2	156.7	H-Bond (Protein Donor)	false
O3X	O	HOH- 2002	2.62	165.63	H-Bond (Protein Donor)	false