scPDB - 1s4d entry

Protein Data Bank Entry:

PDB ID : 1s4d

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2004-01-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uroporphyrinogen-III C-methyltransferase
ID:	SUMT_PSEDE
AC:	P21631
Organism:	Pseudomonas denitrificans
Reign:	Bacteria
TaxID:	43306
EC Number:	2.1.1.107

Chains:

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

Ligand binding site composition:

B-Factor:	24.608
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.384	496.125

% Hydrophobic	% Polar
60.54	39.46
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	70.59 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
42.1055	-12.7562	-35.6437

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
N6	O	PRO- 24	2.66	135.05	H-Bond (Ligand Donor)	false
CG	CD1	LEU- 49	3.73	0	Hydrophobic	false
C5'	CD1	LEU- 49	4.16	0	Hydrophobic	false
N	O	ASP- 102	3.03	128.44	H-Bond (Ligand Donor)	false
O	N	ASP- 102	2.85	159.1	H-Bond (Protein Donor)	false
N	O	VAL- 105	2.82	166.34	H-Bond (Ligand Donor)	false
OXT	OG1	THR- 130	2.95	150.66	H-Bond (Protein Donor)	false
OXT	N	ALA- 131	3.05	172.78	H-Bond (Protein Donor)	false
C1'	CB	ALA- 131	4.11	0	Hydrophobic	false
CB	CD2	TYR- 183	4.06	0	Hydrophobic	false
C4'	CD2	TYR- 183	4.27	0	Hydrophobic	false
C1'	CD2	TYR- 183	3.95	0	Hydrophobic	false
SD	SD	MET- 184	4.22	0	Hydrophobic	false
C4'	CG	MET- 184	3.76	0	Hydrophobic	false
O2'	N	MET- 184	3.18	175.01	H-Bond (Protein Donor)	false
N6	O	ALA- 213	3.14	143.07	H-Bond (Ligand Donor)	false
N1	N	ALA- 213	2.8	124.92	H-Bond (Protein Donor)	false
C3'	CB	PRO- 240	3.81	0	Hydrophobic	false
O2'	O	ALA- 241	2.6	153.89	H-Bond (Ligand Donor)	false
C1'	CG1	ILE- 242	4.21	0	Hydrophobic	false