scPDB - 3eq1 entry

Protein Data Bank Entry:

PDB ID : 3eq1

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2008-09-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Porphobilinogen deaminase
ID:	HEM3_HUMAN
AC:	P08397
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.5.1.61

Chains:

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

Ligand binding site composition:

B-Factor:	56.362
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.017	401.625

% Hydrophobic	% Polar
49.58	50.42
According to VolSite

Ligand :

HET Code:	DPM
Formula:	C20H20N2O8
Molecular weight:	416.381 g/mol
DrugBank ID:	DB04517
Buried Surface Area:	64.11 %
Polar Surface area:	192.1 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
30.4607	13.05	16.8865

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
O4B	OG	SER- 96	2.7	156.81	H-Bond (Protein Donor)	false
CHA	CG	LYS- 98	3.97	0	Hydrophobic	false
O1A	NZ	LYS- 98	2.78	154.39	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 98	2.54	158.84	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 98	2.78	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 98	2.54	0	Ionic (Protein Cationic)	false
DuAr	NZ	LYS- 98	3.49	172.75	Pi/Cation	false
DuAr	NZ	LYS- 98	3.78	168.69	Pi/Cation	false
NA	OD1	ASP- 99	3.13	163.79	H-Bond (Ligand Donor)	false
NB	OD2	ASP- 99	3.27	135.04	H-Bond (Ligand Donor)	false
NB	OD1	ASP- 99	3.31	163.62	H-Bond (Ligand Donor)	false
C5A	CB	SER- 147	4.17	0	Hydrophobic	false
C7A	CB	SER- 147	4.23	0	Hydrophobic	false
O2A	OG	SER- 147	3.15	122.6	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 149	2.73	147.98	H-Bond (Protein Donor)	false
O1A	NE	ARG- 149	3.46	125.98	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 149	3.11	125.46	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 149	3.49	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 149	3.19	0	Ionic (Protein Cationic)	false
O1B	NH2	ARG- 150	3.2	138.16	H-Bond (Protein Donor)	false
O1B	NH1	ARG- 150	3.45	130.85	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 150	2.76	151.99	H-Bond (Protein Donor)	false
O2B	NH1	ARG- 150	3.36	127.58	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 150	3.72	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 150	3.47	0	Ionic (Protein Cationic)	false
O3A	CZ	ARG- 173	3.5	0	Ionic (Protein Cationic)	false
O3A	NH1	ARG- 173	2.79	129.46	H-Bond (Protein Donor)	false
C5B	CB	ALA- 189	4.5	0	Hydrophobic	false
C8B	CB	ALA- 189	3.45	0	Hydrophobic	false
O1B	N	ALA- 189	2.55	153.81	H-Bond (Protein Donor)	false
O4B	NH1	ARG- 195	3.42	154	H-Bond (Protein Donor)	false
O3B	N	GLY- 218	2.93	170.52	H-Bond (Protein Donor)	false
CHA	CB	CYS- 261	3.79	0	Hydrophobic	false