scPDB - 3gi2 entry

Protein Data Bank Entry:

PDB ID : 3gi2

Resolution :1.530 Å

Experimental Method : X-ray

Deposition Date : 2009-03-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dihydrofolate reductase
ID:	DYR_HUMAN
AC:	P00374
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.5.1.3

Chains:

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

Ligand binding site composition:

B-Factor:	12.636
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.803	519.750

% Hydrophobic	% Polar
58.44	41.56
According to VolSite

Ligand :

HET Code:	GHW
Formula:	C19H16N4O6S2
Molecular weight:	460.484 g/mol
DrugBank ID:	-
Buried Surface Area:	67.31 %
Polar Surface area:	230.38 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-12.4165	-8.31726	-0.756839

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
S4	CG2	ILE- 7	4.37	0	Hydrophobic	false
SAT	CD2	LEU- 22	3.88	0	Hydrophobic	false
N1	OE2	GLU- 30	2.81	176.27	H-Bond (Ligand Donor)	false
N2	OE1	GLU- 30	2.82	170.36	H-Bond (Ligand Donor)	false
SAT	CE1	PHE- 31	4.26	0	Hydrophobic	false
CAN	CB	PHE- 31	4.26	0	Hydrophobic	false
CAK	CD2	PHE- 34	3.5	0	Hydrophobic	false
CAN	CD	LYS- 35	4.02	0	Hydrophobic	false
C13	CG2	THR- 56	3.63	0	Hydrophobic	false
CAJ	CG1	ILE- 60	4.39	0	Hydrophobic	false
CAL	CG2	ILE- 60	4.24	0	Hydrophobic	false
OAE	ND2	ASN- 64	2.89	150.12	H-Bond (Protein Donor)	false
OAG	NH2	ARG- 70	3.47	133.93	H-Bond (Protein Donor)	false
OAG	NH1	ARG- 70	2.98	159.24	H-Bond (Protein Donor)	false
OAD	NH2	ARG- 70	2.77	159.14	H-Bond (Protein Donor)	false
OAG	CZ	ARG- 70	3.66	0	Ionic (Protein Cationic)	false
OAD	CZ	ARG- 70	3.74	0	Ionic (Protein Cationic)	false
C13	CB	VAL- 115	4.12	0	Hydrophobic	false
S4	CB	VAL- 115	3.94	0	Hydrophobic	false
C13	C4N	NDP- 188	3.34	0	Hydrophobic	false
SAT	C3N	NDP- 188	4.32	0	Hydrophobic	false
O6	O	HOH- 366	2.88	154.51	H-Bond (Protein Donor)	false
OAD	O	HOH- 388	2.93	179.96	H-Bond (Protein Donor)	false