scPDB - 1a4i entry

Protein Data Bank Entry:

PDB ID : 1a4i

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 1998-01-30

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	94 %
B	6 %

Ligand binding site composition:

B-Factor:	17.784
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.329	867.375

% Hydrophobic	% Polar
52.14	47.86
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	49.44 %
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
-4.1874	48.6166	27.9495

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
C4N	CB	THR- 148	4.29	0	Hydrophobic	false
C5N	CG2	THR- 148	4.49	0	Hydrophobic	false
O3B	N	ARG- 173	2.85	161.41	H-Bond (Protein Donor)	false
O1X	NH2	ARG- 173	2.91	147.73	H-Bond (Protein Donor)	false
O2X	NE	ARG- 173	2.86	169.21	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 173	3.68	0	Ionic (Protein Cationic)	false
O2X	CZ	ARG- 173	3.64	0	Ionic (Protein Cationic)	false
O2N	OG	SER- 174	2.6	129.81	H-Bond (Protein Donor)	false
C5N	CG2	ILE- 176	4.33	0	Hydrophobic	false
C5N	CG2	VAL- 177	3.6	0	Hydrophobic	false
O2B	N	SER- 197	3.3	143.81	H-Bond (Protein Donor)	false
O1X	N	SER- 197	3.16	146.69	H-Bond (Protein Donor)	false
O1X	OG	SER- 197	2.55	158.9	H-Bond (Protein Donor)	false
C5D	CB	ALA- 215	4.14	0	Hydrophobic	false
C1B	CG2	THR- 216	4.02	0	Hydrophobic	false
O3D	N	ILE- 238	3.05	174.39	H-Bond (Protein Donor)	false
O2N	O	HOH- 314	2.82	152.79	H-Bond (Protein Donor)	false