scPDB - 4kd7 entry

Protein Data Bank Entry:

PDB ID : 4kd7

Resolution :2.710 Å

Experimental Method : X-ray

Deposition Date : 2013-04-24

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:	27.505
Number of residues:	32
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.100	560.250

% Hydrophobic	% Polar
60.24	39.76
According to VolSite

Ligand :

HET Code:	9DR
Formula:	C21H21N5O
Molecular weight:	359.424 g/mol
DrugBank ID:	-
Buried Surface Area:	69.12 %
Polar Surface area:	99.94 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
26.8459	14.9934	8.96278

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
NAD	O	ILE- 7	2.75	155.43	H-Bond (Ligand Donor)	false
CAK	CD2	LEU- 22	4.19	0	Hydrophobic	false
CAN	CD1	LEU- 22	4.05	0	Hydrophobic	false
N3	OE1	GLU- 30	2.8	178.07	H-Bond (Ligand Donor)	false
N3	OE2	GLU- 30	3.39	127.55	H-Bond (Ligand Donor)	false
NAC	OE2	GLU- 30	2.62	174.25	H-Bond (Ligand Donor)	false
CAA	CD1	PHE- 31	4.37	0	Hydrophobic	false
CAA	CB	PHE- 34	3.83	0	Hydrophobic	false
CAF	CE1	PHE- 34	4.04	0	Hydrophobic	false
CAO	CG2	THR- 56	3.98	0	Hydrophobic	false
CAI	CG2	ILE- 60	3.98	0	Hydrophobic	false
CAL	CG1	ILE- 60	3.95	0	Hydrophobic	false
CAJ	CD2	LEU- 67	3.86	0	Hydrophobic	false
NAD	O	VAL- 115	3.32	130.23	H-Bond (Ligand Donor)	false
CAO	C5N	NDP- 201	3.83	0	Hydrophobic	false
CAE	C4N	NDP- 201	3.44	0	Hydrophobic	false