scPDB - 3tdl entry

Protein Data Bank Entry:

PDB ID : 3tdl

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2011-08-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Serum albumin
ID:	ALBU_HUMAN
AC:	P02768
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:	52.874
Number of residues:	34
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.042	1387.125

% Hydrophobic	% Polar
44.53	55.47
According to VolSite

Ligand :

HET Code:	11D
Formula:	C23H33N2O4S
Molecular weight:	433.584 g/mol
DrugBank ID:	-
Buried Surface Area:	71.14 %
Polar Surface area:	97.92 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
30.635	3.39307	8.51463

Binding mode :

What is Poseview ?

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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
C12	CG	LYS- 199	3.73	0	Hydrophobic	false
C12	CZ	PHE- 211	3.72	0	Hydrophobic	false
C13	CZ	PHE- 211	3.72	0	Hydrophobic	false
C12	CZ3	TRP- 214	3.3	0	Hydrophobic	false
C6	CB	ALA- 215	4.22	0	Hydrophobic	false
O15	NH2	ARG- 218	3.19	120.13	H-Bond (Protein Donor)	false
C4	CD	ARG- 218	3.84	0	Hydrophobic	false
C5	CB	ARG- 218	3.46	0	Hydrophobic	false
C5	CD2	LEU- 219	3.71	0	Hydrophobic	false
C6	CG	LEU- 219	3.89	0	Hydrophobic	false
C19	CD2	LEU- 219	3.57	0	Hydrophobic	false
C18	CZ	PHE- 223	3.78	0	Hydrophobic	false
C19	CE1	PHE- 223	3.94	0	Hydrophobic	false
C13	CD2	LEU- 238	3.47	0	Hydrophobic	false
C19	CD1	LEU- 238	4.22	0	Hydrophobic	false
C2	CD2	LEU- 238	4.36	0	Hydrophobic	false
C6	CD1	LEU- 238	3.76	0	Hydrophobic	false
C21	CD2	LEU- 238	3.7	0	Hydrophobic	false
C25	CD2	LEU- 238	3.65	0	Hydrophobic	false
C26	CG2	VAL- 241	4.36	0	Hydrophobic	false
C13	CB	HIS- 242	4.21	0	Hydrophobic	false
O30	ND1	HIS- 242	3.31	144.71	H-Bond (Protein Donor)	false
C26	CD	ARG- 257	3.98	0	Hydrophobic	false
C23	CD2	LEU- 260	3.73	0	Hydrophobic	false
C21	CD1	ILE- 264	3.84	0	Hydrophobic	false
C23	CB	SER- 287	4.15	0	Hydrophobic	false
C21	CG2	ILE- 290	3.44	0	Hydrophobic	false
N17	O	ALA- 291	3.01	134.98	H-Bond (Ligand Donor)	false
C20	CB	ALA- 291	4.4	0	Hydrophobic	false
C22	CB	ALA- 291	4.37	0	Hydrophobic	false
C9	CB	ALA- 291	3.69	0	Hydrophobic	false
C24	CB	ALA- 291	3.43	0	Hydrophobic	false