eF-site ID 6h4o-D
PDB Code 6h4o
Chain D

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Title Crystal structure of human KDM4A in complex with compound 18a
Classification OXIDOREDUCTASE
Compound Lysine-specific demethylase 4A
Source (KDM4A_HUMAN)
Sequence D:  ESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAG
LAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFT
QYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWK
NLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEGV
NTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSV
PPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLK
KYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNF
ATRRWIEYGKQAVLCSCMVKISMDVFVRKFQPERYKLWKA
GKDNTVIDHTLPTPEAAEFL
Description (1)  Lysine-specific demethylase 4A (E.C.1.14.11.-)


Functional site

1) chain D
residue 75
type
ligand
sequence V
description binding site for residue GOL B 404
source : AC9

2) chain D
residue 76
type
ligand
sequence T
description binding site for residue GOL B 404
source : AC9

3) chain D
residue 77
type
ligand
sequence G
description binding site for residue GOL B 404
source : AC9

4) chain D
residue 126
type
ligand
sequence T
description binding site for residue GOL B 404
source : AC9

5) chain D
residue 127
type
ligand
sequence F
description binding site for residue GOL B 404
source : AC9

6) chain D
residue 188
type
ligand
sequence H
description binding site for residue ZN D 401
source : AD7

7) chain D
residue 190
type
ligand
sequence E
description binding site for residue ZN D 401
source : AD7

8) chain D
residue 276
type
ligand
sequence H
description binding site for residue ZN D 401
source : AD7

9) chain D
residue 234
type
ligand
sequence C
description binding site for residue ZN D 402
source : AD8

10) chain D
residue 240
type
ligand
sequence H
description binding site for residue ZN D 402
source : AD8

11) chain D
residue 306
type
ligand
sequence C
description binding site for residue ZN D 402
source : AD8

12) chain D
residue 308
type
ligand
sequence C
description binding site for residue ZN D 402
source : AD8

13) chain D
residue 132
type
ligand
sequence Y
description binding site for residue FQH D 403
source : AD9

14) chain D
residue 135
type
ligand
sequence D
description binding site for residue FQH D 403
source : AD9

15) chain D
residue 177
type
ligand
sequence Y
description binding site for residue FQH D 403
source : AD9

16) chain D
residue 185
type
ligand
sequence F
description binding site for residue FQH D 403
source : AD9

17) chain D
residue 188
type
ligand
sequence H
description binding site for residue FQH D 403
source : AD9

18) chain D
residue 190
type
ligand
sequence E
description binding site for residue FQH D 403
source : AD9

19) chain D
residue 206
type
ligand
sequence K
description binding site for residue FQH D 403
source : AD9

20) chain D
residue 208
type
ligand
sequence W
description binding site for residue FQH D 403
source : AD9

21) chain D
residue 276
type
ligand
sequence H
description binding site for residue FQH D 403
source : AD9

22) chain D
residue 193
type
ligand
sequence D
description binding site for residue DMS D 404
source : AE1

23) chain D
residue 217
type
ligand
sequence K
description binding site for residue DMS D 404
source : AE1

24) chain D
residue 273
type
ligand
sequence Y
description binding site for residue DMS D 404
source : AE1

25) chain D
residue 299
type
ligand
sequence Y
description binding site for residue DMS D 404
source : AE1

26) chain D
residue 302
type
ligand
sequence Q
description binding site for residue DMS D 404
source : AE1

27) chain D
residue 343
type
ligand
sequence H
description binding site for residue DMS D 404
source : AE1

28) chain D
residue 132
type binding
ligand FQH: 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
sequence Y
description 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one binding site
source pdb_hetatom : FQH_6h4o_D_403

29) chain D
residue 135
type binding
ligand FQH: 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
sequence D
description 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one binding site
source pdb_hetatom : FQH_6h4o_D_403

30) chain D
residue 170
type binding
ligand FQH: 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
sequence G
description 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one binding site
source pdb_hetatom : FQH_6h4o_D_403

31) chain D
residue 175
type binding
ligand FQH: 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
sequence Y
description 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one binding site
source pdb_hetatom : FQH_6h4o_D_403

32) chain D
residue 177
type binding
ligand FQH: 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
sequence Y
description 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one binding site
source pdb_hetatom : FQH_6h4o_D_403

33) chain D
residue 185
type binding
ligand FQH: 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
sequence F
description 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one binding site
source pdb_hetatom : FQH_6h4o_D_403

34) chain D
residue 188
type binding
ligand FQH: 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
sequence H
description 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one binding site
source pdb_hetatom : FQH_6h4o_D_403

35) chain D
residue 190-191
type binding
ligand FQH: 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
sequence ED
description 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one binding site
source pdb_hetatom : FQH_6h4o_D_403

36) chain D
residue 198
type binding
ligand FQH: 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
sequence N
description 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one binding site
source pdb_hetatom : FQH_6h4o_D_403

37) chain D
residue 206
type binding
ligand FQH: 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
sequence K
description 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one binding site
source pdb_hetatom : FQH_6h4o_D_403

38) chain D
residue 208
type binding
ligand FQH: 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
sequence W
description 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one binding site
source pdb_hetatom : FQH_6h4o_D_403

39) chain D
residue 241
type binding
ligand FQH: 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
sequence K
description 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one binding site
source pdb_hetatom : FQH_6h4o_D_403

40) chain D
residue 276
type binding
ligand FQH: 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
sequence H
description 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one binding site
source pdb_hetatom : FQH_6h4o_D_403

41) chain D
residue 280
type binding
ligand FQH: 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
sequence N
description 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one binding site
source pdb_hetatom : FQH_6h4o_D_403

42) chain D
residue 313
type binding
ligand FQH: 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
sequence V
description 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one binding site
source pdb_hetatom : FQH_6h4o_D_403

43) chain D
residue 193
type binding
ligand DMS: DIMETHYL SULFOXIDE
sequence D
description DIMETHYL SULFOXIDE binding site
source pdb_hetatom : DMS_6h4o_D_404

44) chain D
residue 217
type binding
ligand DMS: DIMETHYL SULFOXIDE
sequence K
description DIMETHYL SULFOXIDE binding site
source pdb_hetatom : DMS_6h4o_D_404

45) chain D
residue 273
type binding
ligand DMS: DIMETHYL SULFOXIDE
sequence Y
description DIMETHYL SULFOXIDE binding site
source pdb_hetatom : DMS_6h4o_D_404

46) chain D
residue 299
type binding
ligand DMS: DIMETHYL SULFOXIDE
sequence Y
description DIMETHYL SULFOXIDE binding site
source pdb_hetatom : DMS_6h4o_D_404

47) chain D
residue 302-304
type binding
ligand DMS: DIMETHYL SULFOXIDE
sequence QAV
description DIMETHYL SULFOXIDE binding site
source pdb_hetatom : DMS_6h4o_D_404

48) chain D
residue 341
type binding
ligand DMS: DIMETHYL SULFOXIDE
sequence I
description DIMETHYL SULFOXIDE binding site
source pdb_hetatom : DMS_6h4o_D_404

49) chain D
residue 343
type binding
ligand DMS: DIMETHYL SULFOXIDE
sequence H
description DIMETHYL SULFOXIDE binding site
source pdb_hetatom : DMS_6h4o_D_404


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