scPDB - 5ecc entry

Protein Data Bank Entry:

PDB ID : 5ecc

Resolution :1.870 Å

Experimental Method : X-ray

Deposition Date : 2015-10-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dehydrofolate reductase type I
ID:	A4GRC7_KLEPN
AC:	A4GRC7
Organism:	Klebsiella pneumoniae
Reign:	Bacteria
TaxID:	573
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	38.324
Number of residues:	45
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
1.292	749.250

% Hydrophobic	% Polar
51.35	48.65
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	76.83 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
18.6126	59.947	-24.5296

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
O7N	N	ALA- 7	2.75	177.3	H-Bond (Protein Donor)	false
N7N	O	ALA- 7	2.83	139.1	H-Bond (Ligand Donor)	false
N7N	O	ILE- 14	3.06	161.6	H-Bond (Ligand Donor)	false
O3D	O	GLY- 17	2.61	177.34	H-Bond (Ligand Donor)	false
C3N	CD1	ILE- 20	3.6	0	Hydrophobic	false
C4B	CB	ARG- 44	4.31	0	Hydrophobic	false
O4B	N	ARG- 44	3.34	142.86	H-Bond (Protein Donor)	false
O1X	NH1	ARG- 44	2.76	121.65	H-Bond (Protein Donor)	false
O2X	NH1	ARG- 44	3.39	172.52	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 44	3.99	0	Ionic (Protein Cationic)	false
O5B	N	LYS- 45	3.4	152.43	H-Bond (Protein Donor)	false
C5B	CG	LYS- 45	4.03	0	Hydrophobic	false
O2A	OG1	THR- 46	2.69	154.96	H-Bond (Protein Donor)	false
O2A	N	THR- 46	2.91	145.76	H-Bond (Protein Donor)	false
C5N	CG2	THR- 46	3.8	0	Hydrophobic	false
C1B	CG2	VAL- 61	4.17	0	Hydrophobic	false
O3X	N	ARG- 63	2.91	157.58	H-Bond (Protein Donor)	false
O1A	N	GLY- 98	3.01	134.12	H-Bond (Protein Donor)	false
O2A	N	GLY- 98	3.01	131.41	H-Bond (Protein Donor)	false
O5D	N	GLY- 99	3.11	144.53	H-Bond (Protein Donor)	false
C5B	CB	GLU- 100	4.36	0	Hydrophobic	false
O2N	N	GLU- 100	2.8	152.26	H-Bond (Protein Donor)	false
C5B	CD1	ILE- 101	4.45	0	Hydrophobic	false
C4D	CG2	VAL- 125	4.01	0	Hydrophobic	false