scPDB - 4guu entry

Protein Data Bank Entry:

PDB ID : 4guu

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2012-08-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Lysine-specific histone demethylase 1B
ID:	KDM1B_HUMAN
AC:	Q8NB78
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1

Chains:

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

Ligand binding site composition:

B-Factor:	26.295
Number of residues:	75
Including
Standard Amino Acids:	70
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.122	1539.000

% Hydrophobic	% Polar
44.96	55.04
According to VolSite

Ligand :

HET Code:	FA9
Formula:	C36H41N9O16P2
Molecular weight:	917.709 g/mol
DrugBank ID:	-
Buried Surface Area:	82.07 %
Polar Surface area:	389.32 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	8
Rings:	8
Aromatic rings:	4
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
27.7361	1.75203	16.6076

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
C4'	CG	PRO- 392	4.29	0	Hydrophobic	false
O1P	N	ALA- 393	2.97	162.42	H-Bond (Protein Donor)	false
OA3	OE1	GLU- 412	2.85	164.81	H-Bond (Ligand Donor)	false
OA3	OE2	GLU- 412	3.32	120.22	H-Bond (Ligand Donor)	false
OA2	OE2	GLU- 412	2.56	157.88	H-Bond (Ligand Donor)	false
N3A	N	ALA- 413	3.14	139.93	H-Bond (Protein Donor)	false
C8M	CG	ARG- 420	3.58	0	Hydrophobic	false
C9	CB	ARG- 420	4.22	0	Hydrophobic	false
C3'	CB	ARG- 420	4	0	Hydrophobic	false
O3P	NH2	ARG- 420	3.12	139.69	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 420	3.07	137	H-Bond (Protein Donor)	false
O1A	NE	ARG- 420	2.78	156.79	H-Bond (Protein Donor)	false
O2A	N	ARG- 420	2.77	170.29	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 420	3.35	0	Ionic (Protein Cationic)	false
C9A	CB	ALA- 436	3.75	0	Hydrophobic	false
C2'	CB	ALA- 436	4.01	0	Hydrophobic	false
O4	N	GLN- 437	2.85	159.41	H-Bond (Protein Donor)	false
O4	N	ILE- 438	2.86	152.88	H-Bond (Protein Donor)	false
N3	O	ILE- 438	2.83	176.26	H-Bond (Ligand Donor)	false
C2B	CZ	TYR- 545	4.3	0	Hydrophobic	false
O1B	OH	TYR- 545	3.08	127.73	H-Bond (Protein Donor)	false
N1A	N	VAL- 598	3	159.91	H-Bond (Protein Donor)	false
N6A	O	VAL- 598	3.1	160.98	H-Bond (Ligand Donor)	false
CA5	CG	PRO- 628	4.15	0	Hydrophobic	false
C7M	CG1	ILE- 659	3.78	0	Hydrophobic	false
C6	CD1	ILE- 659	3.73	0	Hydrophobic	false
C8M	CE2	TRP- 757	3.92	0	Hydrophobic	false
CA2	CB	TRP- 762	4.18	0	Hydrophobic	false
CA2	CG1	ILE- 763	4.33	0	Hydrophobic	false
C8M	CB	ALA- 766	3.74	0	Hydrophobic	false
C3B	CE2	TYR- 767	4.32	0	Hydrophobic	false
C1'	CD2	TYR- 767	3.86	0	Hydrophobic	false
CB2	CE2	TYR- 767	3.17	0	Hydrophobic	false
C5'	CG	GLU- 795	3.96	0	Hydrophobic	false
O2P	N	GLU- 795	3.11	152.68	H-Bond (Protein Donor)	false
CB5	CB	GLN- 803	3.84	0	Hydrophobic	false
CB5	CG2	THR- 804	3.85	0	Hydrophobic	false
O2	N	VAL- 805	3.06	160.29	H-Bond (Protein Donor)	false
C2'	CG2	VAL- 805	3.76	0	Hydrophobic	false
C5'	CB	ALA- 808	3.82	0	Hydrophobic	false
O1P	O	HOH- 1102	3.05	147.88	H-Bond (Protein Donor)	false
OA3	O	HOH- 1112	3.12	179.99	H-Bond (Protein Donor)	false
O2	O	HOH- 1246	3.07	179.95	H-Bond (Protein Donor)	false