scPDB - 4kl9 entry

Protein Data Bank Entry:

PDB ID : 4kl9

Resolution :1.390 Å

Experimental Method : X-ray

Deposition Date : 2013-05-07

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_MYCTU
AC:	P9WNX1
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	1.5.1.3

Chains:

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

Ligand binding site composition:

B-Factor:	21.239
Number of residues:	43
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.271	1211.625

% Hydrophobic	% Polar
49.86	50.14
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	70.01 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
12.7737	3.38979	15.0992

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
O7N	N	ALA- 7	2.78	167.84	H-Bond (Protein Donor)	false
N7N	O	ALA- 7	2.94	147.79	H-Bond (Ligand Donor)	false
N7N	O	ILE- 14	2.97	153.77	H-Bond (Ligand Donor)	false
O3D	O	ASP- 19	2.99	137.77	H-Bond (Ligand Donor)	false
O2D	O	ASP- 19	3.29	128.7	H-Bond (Ligand Donor)	false
C3N	CD1	ILE- 20	3.58	0	Hydrophobic	false
C4B	CB	ARG- 44	4.31	0	Hydrophobic	false
O4B	N	ARG- 44	3.38	147.78	H-Bond (Protein Donor)	false
O2X	NH2	ARG- 44	2.72	173.56	H-Bond (Protein Donor)	false
O3X	NE	ARG- 44	2.95	163.95	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 44	3.54	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 44	3.83	0	Ionic (Protein Cationic)	false
O5B	N	ARG- 45	3.26	147.38	H-Bond (Protein Donor)	false
O1N	NH1	ARG- 45	2.99	158.49	H-Bond (Protein Donor)	false
C5B	CD	ARG- 45	4.05	0	Hydrophobic	false
C4B	CG	ARG- 45	4.3	0	Hydrophobic	false
C5D	CB	ARG- 45	4.15	0	Hydrophobic	false
O1A	OG1	THR- 46	2.74	158.13	H-Bond (Protein Donor)	false
O1A	N	THR- 46	2.97	136.71	H-Bond (Protein Donor)	false
C5N	CG2	THR- 46	3.88	0	Hydrophobic	false
C1B	CG	LEU- 65	4.5	0	Hydrophobic	false
O3X	OG	SER- 66	2.67	169.9	H-Bond (Protein Donor)	false
O1X	N	ARG- 67	2.94	158.69	H-Bond (Protein Donor)	false
O3X	NE2	GLN- 68	3.02	172.69	H-Bond (Protein Donor)	false
O1A	N	GLY- 96	3.03	127.02	H-Bond (Protein Donor)	false
O2A	N	GLY- 96	3.08	136.95	H-Bond (Protein Donor)	false
O5D	N	GLY- 97	3.21	145.33	H-Bond (Protein Donor)	false
C5B	CB	GLN- 98	4.1	0	Hydrophobic	false
O2N	N	GLN- 98	2.82	150.36	H-Bond (Protein Donor)	false
O2A	N	VAL- 99	3.27	153.77	H-Bond (Protein Donor)	false
C4D	CB	ALA- 126	3.94	0	Hydrophobic	false