scPDB - 3och entry

Protein Data Bank Entry:

PDB ID : 3och

Resolution :1.790 Å

Experimental Method : X-ray

Deposition Date : 2010-08-10

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_ECOLI
AC:	P0ABQ4
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	1.5.1.3

Chains:

Chain Name:	Percentage of Residues within binding site
A	48 %
B	52 %

Ligand binding site composition:

B-Factor:	13.949
Number of residues:	65
Including
Standard Amino Acids:	64
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.242	1228.500

% Hydrophobic	% Polar
44.78	55.22
According to VolSite

Ligand :

HET Code:	2MX
Formula:	C49H60N18O8
Molecular weight:	1029.117 g/mol
DrugBank ID:	-
Buried Surface Area:	51.47 %
Polar Surface area:	410.34 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	8
Rings:	6
Aromatic rings:	6
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	28

Mass center Coordinates

X	Y	Z
27.3867	13.9717	-1.78596

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
NAF	O	ILE- 5	2.82	154.44	H-Bond (Ligand Donor)	false
NAD	OD1	ASP- 27	2.77	178.9	H-Bond (Ligand Donor)	false
NAD	OD2	ASP- 27	3.45	126.81	H-Bond (Ligand Donor)	false
NBS	OD2	ASP- 27	2.59	176.64	H-Bond (Ligand Donor)	false
CBI	CD1	LEU- 28	4.07	0	Hydrophobic	false
CBK	CB	LEU- 28	4.36	0	Hydrophobic	false
CAQ	CD2	LEU- 28	4	0	Hydrophobic	false
CBK	CD	LYS- 32	4.2	0	Hydrophobic	false
CBM	CG2	THR- 46	4.15	0	Hydrophobic	false
CAB	CB	SER- 49	3.72	0	Hydrophobic	false
CAB	CG1	ILE- 50	4.02	0	Hydrophobic	false
CBM	CG1	ILE- 50	4.01	0	Hydrophobic	false
CAU	CG1	ILE- 50	3.75	0	Hydrophobic	false
CAR	CG2	ILE- 50	4.39	0	Hydrophobic	false
CCO	CG1	ILE- 50	3.47	0	Hydrophobic	false
OAH	NH2	ARG- 52	3.41	125.87	H-Bond (Protein Donor)	false
OAL	NH2	ARG- 52	2.97	160.55	H-Bond (Protein Donor)	false
CAQ	CD2	LEU- 54	3.85	0	Hydrophobic	false
OAJ	CZ	ARG- 57	3.61	0	Ionic (Protein Cationic)	false
OAN	CZ	ARG- 57	3.54	0	Ionic (Protein Cationic)	false
OAJ	NH2	ARG- 57	2.69	170.47	H-Bond (Protein Donor)	false
OAN	NH2	ARG- 57	3.43	129.99	H-Bond (Protein Donor)	false
OAN	NH1	ARG- 57	2.81	163.63	H-Bond (Protein Donor)	false
NAF	O	ILE- 94	2.89	138.12	H-Bond (Ligand Donor)	false
N4	O	ILE- 205	3.04	160.89	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 227	2.65	168.61	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 227	3.45	127.19	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 227	2.86	176	H-Bond (Ligand Donor)	false
CG	CB	LEU- 228	3.51	0	Hydrophobic	false
CAO	CD2	LEU- 228	3.82	0	Hydrophobic	false
CB	CB	LYS- 232	4.12	0	Hydrophobic	false
OAL	O	HOH- 235	2.86	121.11	H-Bond (Protein Donor)	false
C9	CG2	THR- 246	4.37	0	Hydrophobic	false
CAA	CB	SER- 249	3.86	0	Hydrophobic	false
C9	CG1	ILE- 250	4.04	0	Hydrophobic	false
CAA	CG1	ILE- 250	4.22	0	Hydrophobic	false
CCN	CG1	ILE- 250	3.69	0	Hydrophobic	false
OAK	NH2	ARG- 252	2.98	161.45	H-Bond (Protein Donor)	false
OAK	NH1	ARG- 252	3.37	139.1	H-Bond (Protein Donor)	false
CAO	CD2	LEU- 254	3.88	0	Hydrophobic	false
O	NH2	ARG- 257	3.32	133.22	H-Bond (Protein Donor)	false
O	NH1	ARG- 257	2.8	158.59	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 257	2.71	164.56	H-Bond (Protein Donor)	false
O	CZ	ARG- 257	3.5	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 257	3.67	0	Ionic (Protein Cationic)	false
N4	O	ILE- 294	2.94	127.59	H-Bond (Ligand Donor)	false