scPDB - 1kmv entry

Protein Data Bank Entry:

PDB ID : 1kmv

Resolution :1.050 Å

Experimental Method : X-ray

Deposition Date : 2001-12-17

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:	12.585
Number of residues:	28
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.983	479.250

% Hydrophobic	% Polar
62.68	37.32
According to VolSite

Ligand :

HET Code:	LII
Formula:	C18H19N5O2
Molecular weight:	337.376 g/mol
DrugBank ID:	DB03060
Buried Surface Area:	60.24 %
Polar Surface area:	109.17 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
11.6472	23.6181	33.8563

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
N4	O	ILE- 7	2.95	160.29	H-Bond (Ligand Donor)	false
C6	CD2	LEU- 22	4.3	0	Hydrophobic	false
C6'	CD1	LEU- 22	4.29	0	Hydrophobic	false
N1	OE2	GLU- 30	2.78	178.98	H-Bond (Ligand Donor)	false
N16	OE1	GLU- 30	2.77	175.35	H-Bond (Ligand Donor)	false
C5X	CZ	PHE- 31	4.33	0	Hydrophobic	false
C5A	CE1	PHE- 34	4.15	0	Hydrophobic	false
C2X	CE2	PHE- 34	3.24	0	Hydrophobic	false
C5A	CG2	THR- 56	4.05	0	Hydrophobic	false
C2'	CG1	ILE- 60	4.25	0	Hydrophobic	false
C5X	CG	PRO- 61	3.69	0	Hydrophobic	false
C5'	CG	PRO- 61	3.98	0	Hydrophobic	false
C5A	CB	VAL- 115	4.29	0	Hydrophobic	false
N4	O	VAL- 115	2.97	136.75	H-Bond (Ligand Donor)	false
C5A	C4N	NDP- 202	3.71	0	Hydrophobic	false
C5	C4N	NDP- 202	3.73	0	Hydrophobic	false