scPDB - 3t8x entry

Protein Data Bank Entry:

PDB ID : 3t8x

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2011-08-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	T-cell surface glycoprotein CD1b
ID:	CD1B_HUMAN
AC:	P29016
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:	28.627
Number of residues:	45
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.152	1572.750

% Hydrophobic	% Polar
79.61	20.39
According to VolSite

Ligand :

HET Code:	T8X
Formula:	C56H103O16S
Molecular weight:	1064.472 g/mol
DrugBank ID:	-
Buried Surface Area:	46.62 %
Polar Surface area:	256.24 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	5
Rings:	2
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	45

Mass center Coordinates

X	Y	Z
33.9888	-50.8462	32.1652

Binding mode :

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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
C52	CE2	PHE- 10	3.95	0	Hydrophobic	false
C56	CE2	PHE- 10	4	0	Hydrophobic	false
C49	CG2	VAL- 12	4.18	0	Hydrophobic	false
C56	CD1	LEU- 66	4.15	0	Hydrophobic	false
C29	CG2	ILE- 69	4.16	0	Hydrophobic	false
C33	CG2	ILE- 69	3.71	0	Hydrophobic	false
C25	CE1	PHE- 70	4.25	0	Hydrophobic	false
C49	CZ	PHE- 70	4.41	0	Hydrophobic	false
C34	CG1	VAL- 72	4.42	0	Hydrophobic	false
C54	CG1	VAL- 72	3.96	0	Hydrophobic	false
C18	CG1	VAL- 72	4.35	0	Hydrophobic	false
C27	CG	TYR- 73	4.42	0	Hydrophobic	false
C28	CD1	TYR- 73	4.14	0	Hydrophobic	false
C29	CB	TYR- 73	3.87	0	Hydrophobic	false
C31	CB	TYR- 73	4.08	0	Hydrophobic	false
C54	CB	TYR- 73	3.52	0	Hydrophobic	false
C10	CE1	TYR- 73	4	0	Hydrophobic	false
C13	CE1	TYR- 73	3.79	0	Hydrophobic	false
C14	CD2	PHE- 77	4.47	0	Hydrophobic	false
C15	CB	PHE- 77	4.35	0	Hydrophobic	false
C13	CD2	PHE- 77	3.93	0	Hydrophobic	false
O10	NH1	ARG- 79	2.88	162.13	H-Bond (Protein Donor)	false
C15	CG	GLU- 80	4.31	0	Hydrophobic	false
C46	CG	GLU- 80	4.05	0	Hydrophobic	false
O13	OE2	GLU- 80	3.37	172.51	H-Bond (Ligand Donor)	false
C23	CB	ALA- 100	3.85	0	Hydrophobic	false
C7	CD2	LEU- 114	4.27	0	Hydrophobic	false
C9	CD1	LEU- 114	4.37	0	Hydrophobic	false
C24	CD1	LEU- 114	4.03	0	Hydrophobic	false
C26	CD1	LEU- 114	4.11	0	Hydrophobic	false
C7	CD1	LEU- 124	4.38	0	Hydrophobic	false
C7	CG2	VAL- 126	3.66	0	Hydrophobic	false
C12	CZ	PHE- 144	4.21	0	Hydrophobic	false
C8	CD1	ILE- 148	3.28	0	Hydrophobic	false
C11	CD1	ILE- 148	3.35	0	Hydrophobic	false
C21	CD1	TYR- 151	3.83	0	Hydrophobic	false
C46	CE1	TYR- 151	3.91	0	Hydrophobic	false
C11	CG2	ILE- 154	3.9	0	Hydrophobic	false
C21	CD1	ILE- 154	4.03	0	Hydrophobic	false
C14	CD1	ILE- 154	3.53	0	Hydrophobic	false
C16	CD1	ILE- 154	4.23	0	Hydrophobic	false
C7	CE	MET- 155	4.28	0	Hydrophobic	false
C30	CG2	THR- 157	4.04	0	Hydrophobic	false
C32	CG2	THR- 157	4.14	0	Hydrophobic	false
C9	CG2	VAL- 158	4.07	0	Hydrophobic	false
C26	CG2	VAL- 158	4.42	0	Hydrophobic	false
C28	CG2	VAL- 158	3.91	0	Hydrophobic	false
C30	CG2	VAL- 158	4.36	0	Hydrophobic	false
C25	CD1	LEU- 161	4.1	0	Hydrophobic	false
C51	CB	LEU- 161	4.2	0	Hydrophobic	false
C23	CB	LEU- 161	3.73	0	Hydrophobic	false
C23	CD2	LEU- 162	3.66	0	Hydrophobic	false
C55	CG2	THR- 165	4.08	0	Hydrophobic	false
C51	CB	CYS- 166	4.11	0	Hydrophobic	false
C56	CG	TYR- 169	4.03	0	Hydrophobic	false