scPDB - 3td8 entry

Protein Data Bank Entry:

PDB ID : 3td8

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2011-08-10

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_PNECA
AC:	P16184
Organism:	Pneumocystis carinii
Reign:	Eukaryota
TaxID:	4754
EC Number:	1.5.1.3

Chains:

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

Ligand binding site composition:

B-Factor:	35.873
Number of residues:	37
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.441	563.625

% Hydrophobic	% Polar
76.65	23.35
According to VolSite

Ligand :

HET Code:	D2R
Formula:	C22H22N5O3
Molecular weight:	404.442 g/mol
DrugBank ID:	-
Buried Surface Area:	72.43 %
Polar Surface area:	140.07 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
14.2517	1.7759	10.9991

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
NAD	O	ILE- 10	3.04	166.79	H-Bond (Ligand Donor)	false
NAC	O	VAL- 11	3.41	131.1	H-Bond (Ligand Donor)	false
CAA	CD1	LEU- 25	4.32	0	Hydrophobic	false
CBA	CD2	LEU- 25	4.22	0	Hydrophobic	false
CAY	CD2	LEU- 25	3.54	0	Hydrophobic	false
N3	OE1	GLU- 32	2.79	172.78	H-Bond (Ligand Donor)	false
NAC	OE2	GLU- 32	2.75	168.66	H-Bond (Ligand Donor)	false
NAC	OE1	GLU- 32	3.47	131.52	H-Bond (Ligand Donor)	false
CAZ	CD1	ILE- 33	4.49	0	Hydrophobic	false
CBA	CD1	ILE- 33	4.43	0	Hydrophobic	false
CAG	CD1	ILE- 33	3.65	0	Hydrophobic	false
CAN	CG2	ILE- 33	3.74	0	Hydrophobic	false
CAB	CZ	PHE- 36	3.88	0	Hydrophobic	false
DuAr	DuAr	PHE- 36	3.94	0	Aromatic Face/Face	false
CAY	CB	SER- 64	4.33	0	Hydrophobic	false
CBB	CG1	ILE- 65	4.12	0	Hydrophobic	false
CAJ	CG	PRO- 66	4.42	0	Hydrophobic	false
CAG	CD2	PHE- 69	4.39	0	Hydrophobic	false
CAM	CG	PHE- 69	3.9	0	Hydrophobic	false
CAO	CD1	PHE- 69	3.99	0	Hydrophobic	false
CAO	CD2	LEU- 72	4.05	0	Hydrophobic	false
OAE	CZ	ARG- 75	3.79	0	Ionic (Protein Cationic)	false
OAF	CZ	ARG- 75	3.77	0	Ionic (Protein Cationic)	false
OAE	NH1	ARG- 75	3.08	164.08	H-Bond (Protein Donor)	false
OAF	NH2	ARG- 75	2.83	168.19	H-Bond (Protein Donor)	false
CAB	CD1	ILE- 123	4.04	0	Hydrophobic	false
NAD	O	ILE- 123	2.78	121.99	H-Bond (Ligand Donor)	false
CAA	C2D	NDP- 301	3.41	0	Hydrophobic	false
CAB	C4N	NDP- 301	3.69	0	Hydrophobic	false