scPDB - 4kak entry

Protein Data Bank Entry:

PDB ID : 4kak

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2013-04-22

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:	10.385
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.062	583.875

% Hydrophobic	% Polar
63.58	36.42
According to VolSite

Ligand :

HET Code:	06U
Formula:	C22H23N5O
Molecular weight:	373.451 g/mol
DrugBank ID:	-
Buried Surface Area:	69.18 %
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
-14.8155	-2.98607	21.9373

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
NAJ	O	ILE- 7	2.98	164.18	H-Bond (Ligand Donor)	false
CAP	CD2	LEU- 22	4.44	0	Hydrophobic	false
CBB	CG	LEU- 22	4.44	0	Hydrophobic	false
N3	OE2	GLU- 30	2.8	168.39	H-Bond (Ligand Donor)	false
NAH	OE1	GLU- 30	2.66	179.14	H-Bond (Ligand Donor)	false
CAZ	CD1	PHE- 31	4.04	0	Hydrophobic	false
CAI	CG	PHE- 34	4.47	0	Hydrophobic	false
CAN	CZ	PHE- 34	4.1	0	Hydrophobic	false
CAZ	CB	PHE- 34	3.79	0	Hydrophobic	false
C5	CD1	PHE- 34	3.5	0	Hydrophobic	false
CAK	CE1	PHE- 34	3.83	0	Hydrophobic	false
CAN	CG2	THR- 56	3.79	0	Hydrophobic	false
CAN	CG1	ILE- 60	4.29	0	Hydrophobic	false
CAT	CG1	ILE- 60	4	0	Hydrophobic	false
CAU	CG2	ILE- 60	4.17	0	Hydrophobic	false
CAA	CG	PRO- 61	4.33	0	Hydrophobic	false
CAV	CD2	LEU- 67	3.61	0	Hydrophobic	false
NAJ	O	VAL- 115	3.42	128.12	H-Bond (Ligand Donor)	false
CAN	CG2	VAL- 115	4.12	0	Hydrophobic	false
CAL	C4N	NDP- 201	3.41	0	Hydrophobic	false
CAM	C5N	NDP- 201	3.77	0	Hydrophobic	false