eF-site ID 6nji-AB
PDB Code 6nji
Chain A, B

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Title Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-49
Classification HYDROLASE/HYDROLASE INHIBITOR
Compound cAMP-specific 3',5'-cyclic phosphodiesterase 4D
Source (PDE4D_HUMAN)
Sequence A:  EQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIF
QERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAA
DVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPG
VSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENC
DIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTM
VETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPL
QLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVE
KSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWY
QSTIPQNQVSEFISNTFLD
B:  QEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQ
ERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAAD
VVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGV
SNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCD
IFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMV
ETKKVTVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYR
QWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQV
GFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTI
PQNQVSEFISNTFLD
Description (1)  cAMP-specific 3',5'-cyclic phosphodiesterase 4D (E.C.3.1.4.53)


Functional site

1) chain A
residue 330
type
ligand
sequence H
description binding site for residue ZN A 700
source : AC1

2) chain A
residue 366
type
ligand
sequence H
description binding site for residue ZN A 700
source : AC1

3) chain A
residue 367
type
ligand
sequence D
description binding site for residue ZN A 700
source : AC1

4) chain A
residue 484
type
ligand
sequence D
description binding site for residue ZN A 700
source : AC1

5) chain A
residue 367
type
ligand
sequence D
description binding site for residue MG A 701
source : AC2

6) chain A
residue 487
type
ligand
sequence N
description binding site for residue KR4 A 702
source : AC3

7) chain A
residue 499
type
ligand
sequence T
description binding site for residue KR4 A 702
source : AC3

8) chain A
residue 535
type
ligand
sequence Q
description binding site for residue KR4 A 702
source : AC3

9) chain A
residue 538
type
ligand
sequence F
description binding site for residue KR4 A 702
source : AC3

10) chain A
residue 599
type
ligand
sequence F
description binding site for residue KR4 A 702
source : AC3

11) chain B
residue 330
type
ligand
sequence H
description binding site for residue ZN B 700
source : AC4

12) chain B
residue 366
type
ligand
sequence H
description binding site for residue ZN B 700
source : AC4

13) chain B
residue 367
type
ligand
sequence D
description binding site for residue ZN B 700
source : AC4

14) chain B
residue 484
type
ligand
sequence D
description binding site for residue ZN B 700
source : AC4

15) chain B
residue 367
type
ligand
sequence D
description binding site for residue MG B 701
source : AC5

16) chain B
residue 487
type
ligand
sequence N
description binding site for residue KR4 B 702
source : AC6

17) chain B
residue 499
type
ligand
sequence T
description binding site for residue KR4 B 702
source : AC6

18) chain B
residue 535
type
ligand
sequence Q
description binding site for residue KR4 B 702
source : AC6

19) chain B
residue 538
type
ligand
sequence F
description binding site for residue KR4 B 702
source : AC6

20) chain B
residue 599
type
ligand
sequence F
description binding site for residue KR4 B 702
source : AC6

21) chain A
residue 325-326
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence YH
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_A_702

22) chain A
residue 370
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence H
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_A_702

23) chain A
residue 374
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence S
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_A_702

24) chain A
residue 439
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence M
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_A_702

25) chain A
residue 485
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence L
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_A_702

26) chain A
residue 487-488
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence NP
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_A_702

27) chain A
residue 495
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence Y
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_A_702

28) chain A
residue 498-499
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence WT
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_A_702

29) chain A
residue 502-503
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence IM
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_A_702

30) chain A
residue 505-506
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence EF
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_A_702

31) chain A
residue 523
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence M
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_A_702

32) chain A
residue 534-535
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence SQ
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_A_702

33) chain A
residue 538
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence F
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_A_702

34) chain A
residue 596
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence V
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_A_702

35) chain A
residue 599-600
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence FI
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_A_702

36) chain A
residue 603-604
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence TF
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_A_702

37) chain B
residue 325-326
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence YH
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_B_702

38) chain B
residue 370
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence H
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_B_702

39) chain B
residue 373-374
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence VS
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_B_702

40) chain B
residue 439
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence M
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_B_702

41) chain B
residue 485
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence L
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_B_702

42) chain B
residue 487-488
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence NP
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_B_702

43) chain B
residue 495
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence Y
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_B_702

44) chain B
residue 498-499
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence WT
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_B_702

45) chain B
residue 502-503
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence IM
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_B_702

46) chain B
residue 506
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence F
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_B_702

47) chain B
residue 523
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence M
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_B_702

48) chain B
residue 534-535
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence SQ
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_B_702

49) chain B
residue 538
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence F
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_B_702

50) chain B
residue 596
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence V
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_B_702

51) chain B
residue 599-600
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence FI
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_B_702

52) chain B
residue 603-604
type binding
ligand KR4: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol
sequence TF
description 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol binding site
source pdb_hetatom : KR4_6nji_B_702


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