scPDB - 1dib entry

Protein Data Bank Entry:

PDB ID : 1dib

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 1999-11-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	C-1-tetrahydrofolate synthase, cytoplasmic
ID:	C1TC_HUMAN
AC:	P11586
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.5.1.5

Chains:

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

Ligand binding site composition:

B-Factor:	20.205
Number of residues:	33
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:	NAP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.787	695.250

% Hydrophobic	% Polar
50.00	50.00
According to VolSite

Ligand :

HET Code:	L34
Formula:	C20H19N7O7
Molecular weight:	469.408 g/mol
DrugBank ID:	-
Buried Surface Area:	51.67 %
Polar Surface area:	216.96 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	4
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
1.49371	57.0081	18.9742

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
C2B	CB	TYR- 52	4.37	0	Hydrophobic	false
OX	NZ	LYS- 56	3.18	120.79	H-Bond (Protein Donor)	false
N2A	O	VAL- 99	2.96	157.21	H-Bond (Ligand Donor)	false
N2A	OD1	ASP- 125	3.21	127.53	H-Bond (Ligand Donor)	false
N3	OD1	ASP- 125	2.67	150.27	H-Bond (Ligand Donor)	false
CB	CB	PRO- 272	4.23	0	Hydrophobic	false
OXT	N	GLY- 273	2.85	151.56	H-Bond (Protein Donor)	false
C2B	CG2	THR- 279	4.47	0	Hydrophobic	false
C3B	CG2	VAL- 280	3.34	0	Hydrophobic	false
C7	C5N	NAP- 2001	4.49	0	Hydrophobic	false