scPDB - 4tmc entry

Protein Data Bank Entry:

PDB ID : 4tmc

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2014-05-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Old yellow enzyme
ID:	Q6I7B7_KLUMA
AC:	Q6I7B7
Organism:	Kluyveromyces marxianus
Reign:	Eukaryota
TaxID:	4911
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	68.119
Number of residues:	45
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.871	695.250

% Hydrophobic	% Polar
49.03	50.97
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	73.34 %
Polar Surface area:	217.05 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-16.7442	17.7035	87.6057

Binding mode :

What is Poseview ?

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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
O2'	O	ALA- 35	2.88	165.8	H-Bond (Ligand Donor)	false
C2'	CD2	LEU- 36	4.08	0	Hydrophobic	false
C9	CD2	LEU- 36	3.89	0	Hydrophobic	false
O4	OG1	THR- 37	2.63	150.74	H-Bond (Protein Donor)	false
N5	N	THR- 37	2.59	174.14	H-Bond (Protein Donor)	false
N5	OG1	THR- 37	3.48	132.54	H-Bond (Protein Donor)	false
C6	CB	THR- 37	4.07	0	Hydrophobic	false
O4	N	GLY- 72	3.12	153.36	H-Bond (Protein Donor)	false
O2	NE2	GLN- 114	2.86	175.24	H-Bond (Protein Donor)	false
N3	OE1	GLN- 114	2.86	165.29	H-Bond (Ligand Donor)	false
O2	NH1	ARG- 243	2.73	141.26	H-Bond (Protein Donor)	false
O2'	NH2	ARG- 243	3.43	130.18	H-Bond (Protein Donor)	false
O2'	NH1	ARG- 243	3.04	143.76	H-Bond (Protein Donor)	false
O3'	NH2	ARG- 243	3.01	130.78	H-Bond (Protein Donor)	false
O3'	NH1	ARG- 243	3.4	122.16	H-Bond (Protein Donor)	false
C5'	CG1	VAL- 292	4	0	Hydrophobic	false
C8M	CB	PRO- 295	4.42	0	Hydrophobic	false
C9	CB	PRO- 295	3.96	0	Hydrophobic	false
C1'	CB	PRO- 295	4.24	0	Hydrophobic	false
C4'	CB	PRO- 295	4.04	0	Hydrophobic	false
C3'	CG1	VAL- 323	3.74	0	Hydrophobic	false
C5'	CG1	VAL- 323	4.22	0	Hydrophobic	false
O3P	N	ASN- 325	2.8	163.03	H-Bond (Protein Donor)	false
O1P	N	GLY- 347	2.85	164.92	H-Bond (Protein Donor)	false
C8M	CG	ARG- 348	3.77	0	Hydrophobic	false
O2P	NE	ARG- 348	2.92	163.75	H-Bond (Protein Donor)	false
O2P	N	ARG- 348	2.85	165.57	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 348	2.86	165.14	H-Bond (Protein Donor)	false
O2P	CZ	ARG- 348	3.76	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 348	3.7	0	Ionic (Protein Cationic)	false
C7M	CD1	ILE- 351	4.11	0	Hydrophobic	false
C7M	CD2	PHE- 374	3.65	0	Hydrophobic	false
C8M	CE2	PHE- 374	4.01	0	Hydrophobic	false
C7M	CZ	TYR- 375	3.3	0	Hydrophobic	false
O1P	O	HOH- 713	2.71	162.66	H-Bond (Protein Donor)	false