Receptor
PDB id Resolution Class Description Source Keywords
5E58 2.4 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF CYTOCHROME P450 2B35 FROM DESERT WOODRA LEPIDA IN COMPLEX WITH 4-(4-CHLOROPHENYL)IMIDAZOLE NEOTOMA LEPIDA CYTOCHROME P450; CYP2B35; NEOTOMA LEPIDA; WOODRAT OXIDOREDU
Ref.: STRUCTURE-FUNCTION ANALYSIS OF MAMMALIAN CYP2B ENZY 7-SUBSTITUTED COUMARIN DERIVATIVES AS PROBES: UTILI CRYSTAL STRUCTURES AND MOLECULAR MODELING IN UNDERS XENOBIOTIC METABOLISM. MOL.PHARMACOL. V. 89 435 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
HEM E:501;
B:501;
A:501;
D:501;
F:501;
C:501;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
submit data
616.487 C34 H32 Fe N4 O4 Cc1c2...
CPZ C:502;
A:502;
E:503;
E:502;
F:503;
A:503;
B:502;
C:503;
F:502;
B:503;
D:503;
D:502;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
Kd = 2.3 uM
178.618 C9 H7 Cl N2 c1cc(...
SUC A:504;
Invalid;
none;
submit data
342.296 C12 H22 O11 C([C@...
GOL B:504;
E:505;
C:504;
A:506;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
CM5 E:504;
A:505;
Invalid;
Invalid;
none;
none;
submit data
494.573 C23 H42 O11 C1CCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5E58 2.4 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF CYTOCHROME P450 2B35 FROM DESERT WOODRA LEPIDA IN COMPLEX WITH 4-(4-CHLOROPHENYL)IMIDAZOLE NEOTOMA LEPIDA CYTOCHROME P450; CYP2B35; NEOTOMA LEPIDA; WOODRAT OXIDOREDU
Ref.: STRUCTURE-FUNCTION ANALYSIS OF MAMMALIAN CYP2B ENZY 7-SUBSTITUTED COUMARIN DERIVATIVES AS PROBES: UTILI CRYSTAL STRUCTURES AND MOLECULAR MODELING IN UNDERS XENOBIOTIC METABOLISM. MOL.PHARMACOL. V. 89 435 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 5E58 Kd = 2.3 uM CPZ C9 H7 Cl N2 c1cc(ccc1c....
70% Homology Family (39)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3T3R Ki = 101 uM 9PL C11 H16 N2 O2 CC[C@H]1[C....
2 2FDY - D4G C10 H8 N2 S2 c1cnccc1SS....
3 2FDV Ki = 800 nM D2G C11 H12 N2 O CNCc1ccc(o....
4 4EJH Kd = 4.4 uM 0QA C10 H13 N3 O2 CN(CCCC(=O....
5 3EBS Kd = 21 uM N4E C10 H13 N O2 CCOc1ccc(c....
6 1Z10 Kd = 0.27 uM COU C9 H6 O2 c1ccc2c(c1....
7 4EJI Kd = 4.4 uM 0QA C10 H13 N3 O2 CN(CCCC(=O....
8 2FDU Ki = 14200 nM D1G C12 H14 N2 O CN(C)Cc1cc....
9 2FDW Ki = 130 nM D3G C10 H10 N2 O c1cc(cnc1)....
10 2P85 - IND C8 H7 N c1ccc2c(c1....
11 1Z11 Kd = 1.9 uM 8MO C12 H8 O4 COc1c2c(cc....
12 4EJJ Kd = 470 uM NCT C10 H14 N2 C[N@@]1CCC....
13 4EJG - NCT C10 H14 N2 C[N@@]1CCC....
14 3T3Q Ki = 49 uM 9PL C11 H16 N2 O2 CC[C@H]1[C....
15 5E58 Kd = 2.3 uM CPZ C9 H7 Cl N2 c1cc(ccc1c....
16 1NR6 Kd ~ 50 uM DIF C14 H11 Cl2 N O2 c1ccc(c(c1....
17 1N6B Kd = 20 uM DMZ C17 H17 N3 O2 S Cc1ccc(cc1....
18 4RRT Kd = 1.82 uM 3V4 C10 H16 CC1=CC[C@H....
19 4ZV8 - TMH C10 H16 CC1=CC[C@@....
20 5UEC - 85D C10 H15 Br CC1([C@@H]....
21 3IBD - CPZ C9 H7 Cl N2 c1cc(ccc1c....
22 5UAP - 82S C10 H17 Br C[C@@]12CC....
23 4RQL Kd = 0.08 uM SNE C10 H16 CC(C)[C@@]....
24 4I91 Kd = 0.22 uM TMH C10 H16 CC1=CC[C@@....
25 5UFG - 85D C10 H15 Br CC1([C@@H]....
26 3QOA Kd = 0.21 uM 3QO C12 H11 N c1ccc(cc1)....
27 5UDA - CAE C10 H18 CC1(C2CCC1....
28 2NNJ Ki = 90 nM 225 C18 H19 Cl2 N O4 CCOC(=O)C1....
29 3G5N ic50 = 0.035 uM PB2 C16 H14 N2 c1ccc(cc1)....
30 3TMZ ic50 = 2 uM 06X C20 H25 Cl N2 O5 CCOC(=O)C1....
31 2BDM ic50 = 0.9 uM TMI C22 H18 N2 c1ccc(cc1)....
32 4JLT Kd = 0.7 uM 8PR C19 H20 F N O3 c1cc(ccc1[....
33 4MGJ - CPZ C9 H7 Cl N2 c1cc(ccc1c....
34 1SUO ic50 = 0.04 uM CPZ C9 H7 Cl N2 c1cc(ccc1c....
35 5W0C - 9W6 C15 H12 N4 O4 S2 CCOC(=O)NC....
36 4NZ2 Kd = 2 uM 2QJ C16 H12 Br Cl F3 N O4 S C[C@@](C(=....
37 1R9O - FLP C15 H13 F O2 C[C@@H](c1....
38 5K7K ic50 = 36 nM 6RJ C19 H12 Cl N5 O3 S2 c1cc(c(cc1....
39 3T3Z Ki = 765 uM 9PL C11 H16 N2 O2 CC[C@H]1[C....
50% Homology Family (43)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3T3R Ki = 101 uM 9PL C11 H16 N2 O2 CC[C@H]1[C....
2 2FDY - D4G C10 H8 N2 S2 c1cnccc1SS....
3 2FDV Ki = 800 nM D2G C11 H12 N2 O CNCc1ccc(o....
4 4EJH Kd = 4.4 uM 0QA C10 H13 N3 O2 CN(CCCC(=O....
5 3EBS Kd = 21 uM N4E C10 H13 N O2 CCOc1ccc(c....
6 1Z10 Kd = 0.27 uM COU C9 H6 O2 c1ccc2c(c1....
7 4EJI Kd = 4.4 uM 0QA C10 H13 N3 O2 CN(CCCC(=O....
8 2FDU Ki = 14200 nM D1G C12 H14 N2 O CN(C)Cc1cc....
9 2FDW Ki = 130 nM D3G C10 H10 N2 O c1cc(cnc1)....
10 2P85 - IND C8 H7 N c1ccc2c(c1....
11 1Z11 Kd = 1.9 uM 8MO C12 H8 O4 COc1c2c(cc....
12 4EJJ Kd = 470 uM NCT C10 H14 N2 C[N@@]1CCC....
13 4EJG - NCT C10 H14 N2 C[N@@]1CCC....
14 3T3Q Ki = 49 uM 9PL C11 H16 N2 O2 CC[C@H]1[C....
15 5E58 Kd = 2.3 uM CPZ C9 H7 Cl N2 c1cc(ccc1c....
16 1NR6 Kd ~ 50 uM DIF C14 H11 Cl2 N O2 c1ccc(c(c1....
17 1N6B Kd = 20 uM DMZ C17 H17 N3 O2 S Cc1ccc(cc1....
18 4RRT Kd = 1.82 uM 3V4 C10 H16 CC1=CC[C@H....
19 4ZV8 - TMH C10 H16 CC1=CC[C@@....
20 5UEC - 85D C10 H15 Br CC1([C@@H]....
21 3IBD - CPZ C9 H7 Cl N2 c1cc(ccc1c....
22 5UAP - 82S C10 H17 Br C[C@@]12CC....
23 4RQL Kd = 0.08 uM SNE C10 H16 CC(C)[C@@]....
24 4I91 Kd = 0.22 uM TMH C10 H16 CC1=CC[C@@....
25 5UFG - 85D C10 H15 Br CC1([C@@H]....
26 3QOA Kd = 0.21 uM 3QO C12 H11 N c1ccc(cc1)....
27 5UDA - CAE C10 H18 CC1(C2CCC1....
28 2NNJ Ki = 90 nM 225 C18 H19 Cl2 N O4 CCOC(=O)C1....
29 4XRZ ic50 = 0.37 uM SI6 C16 H16 F2 N4 O S c1cc(c(cc1....
30 4WNU - QDN C20 H24 N2 O2 COc1ccc2c(....
31 4WNV - QI9 C20 H24 N2 O2 COc1ccc2c(....
32 4XRY ic50 = 13.9 uM SI5 C17 H18 F2 N4 O S Cn1cc(cn1)....
33 3G5N ic50 = 0.035 uM PB2 C16 H14 N2 c1ccc(cc1)....
34 3TMZ ic50 = 2 uM 06X C20 H25 Cl N2 O5 CCOC(=O)C1....
35 2BDM ic50 = 0.9 uM TMI C22 H18 N2 c1ccc(cc1)....
36 4JLT Kd = 0.7 uM 8PR C19 H20 F N O3 c1cc(ccc1[....
37 4MGJ - CPZ C9 H7 Cl N2 c1cc(ccc1c....
38 1SUO ic50 = 0.04 uM CPZ C9 H7 Cl N2 c1cc(ccc1c....
39 5W0C - 9W6 C15 H12 N4 O4 S2 CCOC(=O)NC....
40 4NZ2 Kd = 2 uM 2QJ C16 H12 Br Cl F3 N O4 S C[C@@](C(=....
41 1R9O - FLP C15 H13 F O2 C[C@@H](c1....
42 5K7K ic50 = 36 nM 6RJ C19 H12 Cl N5 O3 S2 c1cc(c(cc1....
43 3T3Z Ki = 765 uM 9PL C11 H16 N2 O2 CC[C@H]1[C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CPZ; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 CPZ 1 1
2 PIM 0.526316 0.826087
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5E58; Ligand: CPZ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5e58.bio3) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5E58; Ligand: CPZ; Similar sites found: 33
This union binding pocket(no: 2) in the query (biounit: 5e58.bio3) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3HQP ATP 0.0299 0.41212 2.63692
2 4D8N 0HM 0.01831 0.409 3.13901
3 3RGA ILD 0.03641 0.40017 3.18021
4 3G4G D71 0.01261 0.40868 3.32542
5 1GTE FAD 0.04223 0.42628 3.44828
6 3G58 988 0.009871 0.41448 3.93701
7 2VUT NAD 0.01209 0.41042 3.97727
8 5ECP MET 0.04216 0.41331 4.03587
9 5ECP JAA 0.04216 0.41331 4.03587
10 3AHO 3A2 0.02223 0.40681 4.46247
11 2R5T ANP 0.01646 0.41222 4.82574
12 5BYZ 4WE 0.02616 0.40794 4.88506
13 2ZRU FMN 0.02377 0.40295 5.27383
14 2C6Q NDP 0.0132 0.44837 5.41311
15 1EFV AMP 0.04964 0.41264 5.4902
16 1EFV FAD 0.04964 0.41264 5.4902
17 4XVU ATP 0.01825 0.40659 5.99078
18 1FK8 NAD 0.02707 0.4082 6.22568
19 4F7E 0SH 0.03328 0.41046 7.06714
20 3BXO UPP 0.01776 0.40555 7.11297
21 3B8X G4M 0.00327 0.46601 7.17949
22 3C1X CKK 0.02246 0.40905 7.23861
23 2HF9 GSP 0.0219 0.41178 8.40708
24 1IXE COA 0.01316 0.42206 11.1406
25 1CXZ GSP 0.024 0.40577 11.6279
26 1MH1 GNP 0.03305 0.40207 12.3656
27 4BJ8 BTN 0.02217 0.40168 14.2857
28 4XTR ATP 0.01215 0.41382 16.2162
29 4XTR ADP 0.009879 0.41382 16.2162
30 5EYK 5U5 0.04263 0.40366 18.6441
31 4B7S QLE 0.003232 0.46223 20.4128
32 1EB1 ZAL PRO MMO 0.02533 0.41 33.3333
33 4NKW PLO 0.00969 0.42168 47.4645
Pocket No.: 3; Query (leader) PDB : 5E58; Ligand: CPZ; Similar sites found: 8
This union binding pocket(no: 3) in the query (biounit: 5e58.bio5) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3HQP OXL 0.03429 0.40085 2.63692
2 5X1M DHB 0.03356 0.40514 2.74262
3 2PEL LAT 0.01065 0.4052 2.9661
4 1JNR FAD 0.03695 0.43897 4
5 2W2X GSP 0.01433 0.41695 6.48649
6 2Q7D ANP 0.0281 0.40313 8.09249
7 4ZOM 4Q3 0.02317 0.40012 12
8 3BC1 GNP 0.03085 0.40435 22.0339
Pocket No.: 4; Query (leader) PDB : 5E58; Ligand: CPZ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5e58.bio5) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5E58; Ligand: CPZ; Similar sites found: 15
This union binding pocket(no: 5) in the query (biounit: 5e58.bio2) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4P5Z Q7M 0.02556 0.4116 1.93906
2 4GJ3 0XP 0.01988 0.41502 1.98676
3 5K8S CMP 0.01715 0.40545 2.02703
4 3SXF BK5 0.02412 0.41388 2.06612
5 5VCV 1N1 0.01493 0.40917 2.57235
6 4YZC STU 0.0269 0.40662 2.71605
7 3E8N VRA 0.01198 0.43653 2.93255
8 3E8N ATP 0.01198 0.43653 2.93255
9 1LC8 33P 0.02309 0.43603 3.02198
10 5VC5 96M 0.01645 0.41045 3.11419
11 3KFC 61X 0.04351 0.41107 3.55731
12 2IBY COA 0.02901 0.40918 3.79747
13 1DEK DGP 0.02578 0.4004 4.56432
14 1YF4 CYS TYR PHE GLN ASN CYS PRO ARG GLY NH2 0.02322 0.41496 6.27803
15 4G31 0WH 0.01637 0.42391 6.35452
Pocket No.: 6; Query (leader) PDB : 5E58; Ligand: CPZ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5e58.bio2) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5E58; Ligand: CPZ; Similar sites found: 10
This union binding pocket(no: 7) in the query (biounit: 5e58.bio4) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2H7C COA 0.02144 0.44522 1.41988
2 3GGO NAI 0.03711 0.40726 3.18471
3 3GGO ENO 0.03711 0.40726 3.18471
4 1XG5 NAP 0.03462 0.40583 3.22581
5 2R40 EPH 0.03487 0.40382 8.64662
6 1ZAP A70 0.02118 0.41039 9.64912
7 5GPG RAP 0.01512 0.41384 9.67742
8 4DRJ RAP 0.01423 0.41357 9.72222
9 4DRI RAP 0.004838 0.44851 12.5
10 2F1K NAP 0.0315 0.40181 17.2043
Pocket No.: 8; Query (leader) PDB : 5E58; Ligand: CPZ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 5e58.bio4) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 5E58; Ligand: CPZ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 9) in the query (biounit: 5e58.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 5E58; Ligand: CPZ; Similar sites found: 9
This union binding pocket(no: 10) in the query (biounit: 5e58.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3NVD OAN 0.04508 0.4009 1.62272
2 3O61 GDD 0.01798 0.42241 2.09424
3 2ZB4 5OP 0.02357 0.41422 2.2409
4 2C49 ANP 0.02169 0.40426 2.98013
5 3B6O TMP 0.01349 0.40217 3.64372
6 4P6C RES 0.01585 0.40535 4.20168
7 3RI1 3RH 0.0122 0.41981 5.11182
8 1YKD CMP 0.02321 0.40017 8.54271
9 2BOY BHO 0.01374 0.40511 9.05512
Pocket No.: 11; Query (leader) PDB : 5E58; Ligand: CPZ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 11) in the query (biounit: 5e58.bio6) has 7 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 12; Query (leader) PDB : 5E58; Ligand: CPZ; Similar sites found: 10
This union binding pocket(no: 12) in the query (biounit: 5e58.bio6) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2WYA HMG 0.005748 0.43574 1.73913
2 3S5Y DGJ 0.01925 0.40528 2.76382
3 3APT FAD 0.03957 0.4023 2.90323
4 2PEL LBT 0.01 0.41275 2.9661
5 5M4Q PRO 0.02828 0.4011 3.09917
6 4IKR PVP 0.04549 0.40055 3.34347
7 2WOX NDP 0.04949 0.40485 3.88548
8 2C6Q IMP 0.03894 0.40345 5.41311
9 5HCY 60D 0.04565 0.40898 5.74018
10 2WSB NAD 0.04555 0.40396 6.69291
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