Receptor
PDB id Resolution Class Description Source Keywords
3CM2 2.5 Å EC: 6.3.2.- CRYSTAL STRUCTURE OF XIAP BIR3 DOMAIN IN COMPLEX WITH A SMAC-MIMETIC COMPOUND, SMAC010 HOMO SAPIENS ZINC-FINGER APOPTOSIS CYTOPLASM LIGASE METAL-BINDING PHOSPHOPROTEIN POLYMORPHISM PROTEASE INHIBITOR THIOL PROTEASE INHIBITOR UBL CONJUGATION UBL CONJUGATION PATHWAY
Ref.: TARGETING THE X-LINKED INHIBITOR OF APOPTOSIS PROTEIN THROUGH 4-SUBSTITUTED AZABICYCLO[5.3.0]ALKANE SMAC MIMETICS. STRUCTURE, ACTIVITY, AND RECOGNITION PRINCIPLES. J.MOL.BIOL. V. 384 673 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
X23 A:600;
B:600;
C:600;
D:600;
E:600;
F:600;
G:600;
H:600;
I:600;
J:600;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
ic50 = 970 nM
491.625 C28 H37 N5 O3 CC[C@...
ZN A:502;
B:502;
C:502;
D:502;
E:502;
F:502;
G:502;
H:502;
I:502;
J:502;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3CM2 2.5 Å EC: 6.3.2.- CRYSTAL STRUCTURE OF XIAP BIR3 DOMAIN IN COMPLEX WITH A SMAC-MIMETIC COMPOUND, SMAC010 HOMO SAPIENS ZINC-FINGER APOPTOSIS CYTOPLASM LIGASE METAL-BINDING PHOSPHOPROTEIN POLYMORPHISM PROTEASE INHIBITOR THIOL PROTEASE INHIBITOR UBL CONJUGATION UBL CONJUGATION PATHWAY
Ref.: TARGETING THE X-LINKED INHIBITOR OF APOPTOSIS PROTEIN THROUGH 4-SUBSTITUTED AZABICYCLO[5.3.0]ALKANE SMAC MIMETICS. STRUCTURE, ACTIVITY, AND RECOGNITION PRINCIPLES. J.MOL.BIOL. V. 384 673 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 34 families.
1 3CM2 ic50 = 970 nM X23 C28 H37 N5 O3 CC[C@@H](C....
70% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 23 families.
1 5M6E - 7HT C28 H37 N6 O Cc1cnn(c1)....
2 5M6F ic50 = 220 nM 7HU C25 H35 N4 O2 C[C@@H]1CN....
3 5M6M ic50 = 44 nM 7H8 C28 H38 N5 O2 C[C@@H]1CN....
4 5M6H ic50 = 150 nM 7J6 C28 H38 N5 O3 C[C@@H]1CN....
5 3HL5 - 9JZ C28 H38 N6 O3 C[C@H]1CCN....
6 2VSL Ki = 4 nM MAA LYS PRO PHE n/a n/a
7 1XB0 - ALA VAL PRO ILE ALA GLN LYS n/a n/a
8 3CM2 ic50 = 970 nM X23 C28 H37 N5 O3 CC[C@@H](C....
9 5C7A - 4YE C15 H22 N3 O C[C@@H]1CN....
10 5C3K ic50 = 110 uM 4XF C8 H13 N4 O C[C@@H](C(....
11 5C7D ic50 = 7.7 uM 4YF C14 H20 Cl N4 O C[C@@H]1CN....
12 5C83 ic50 = 0.16 uM 4YN C25 H35 N4 O2 C[C@@H]1CN....
13 5C84 ic50 = 0.64 uM 4YL C18 H28 Cl N4 O2 C[C@@H]1CN....
14 5C0K ic50 = 1200 uM 4WK C8 H18 N3 O2 C[C@@H](C(....
15 5C7C ic50 = 5.5 uM 4YC C17 H25 Cl N3 O C[C@@H]1CN....
50% Homology Family (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 4KJU ic50 = 0.006 uM 1RH C32 H33 N5 O4 C[C@@H](C(....
2 4KJV ic50 = 0.018 uM 1RK C30 H33 N3 O7 C[C@@H](C(....
3 4J48 Ki = 2.41 uM ALA MET ARG VAL n/a n/a
4 4J45 Ki = 1.7 uM ALA THR ALA ALA n/a n/a
5 4J46 Ki = 5.24 uM ALA VAL PRO ILE n/a n/a
6 4J47 Ki = 12.02 uM SER VAL PRO ILE n/a n/a
7 4J44 Ki = 1.87 uM ALA ILE ALA VAL n/a n/a
8 4HY5 ic50 = 1.3 nM 1AQ C31 H45 F2 N5 O5 CCO[C@@H]1....
9 4MTI ic50 = 1.2 nM 2DX C30 H45 N5 O4 CC[C@@H](C....
10 4LGU ic50 = 28 nM 1YH C29 H43 N5 O4 C[C@@H](C(....
11 5M6N - 7H9 C29 H41 F N5 O2 C[C@@H]1CN....
12 5M6H ic50 = 150 nM 7J6 C28 H38 N5 O3 C[C@@H]1CN....
13 3UW5 Ki = 0.014 uM MAA CHG PRO 0DQ n/a n/a
14 3HL5 - 9JZ C28 H38 N6 O3 C[C@H]1CCN....
15 2VSL Ki = 4 nM MAA LYS PRO PHE n/a n/a
16 2I3H Ki = 0.04 uM ALA VAL PRO TRP n/a n/a
17 3GT9 - 516 C29 H36 N4 O2 S C[C@@H](C(....
18 2I3I Ki = 0.05 uM 618 C25 H32 N6 O3 S Cc1cc(n(n1....
19 3F7I - G13 C28 H38 N4 O3 C[C@@H](C(....
20 1XB0 - ALA VAL PRO ILE ALA GLN LYS n/a n/a
21 3CM2 ic50 = 970 nM X23 C28 H37 N5 O3 CC[C@@H](C....
22 4WVU ic50 = 1.97 uM MAA VAL 3V8 PHE HOX n/a n/a
23 4WVT ic50 = 4.87 uM MAA PHE PRO PHE PHE 3V7 n/a n/a
24 4WVS ic50 = 0.54 uM MAA LPH PRO PHE 4LZ n/a n/a
25 5C7A - 4YE C15 H22 N3 O C[C@@H]1CN....
26 5C0K ic50 = 1200 uM 4WK C8 H18 N3 O2 C[C@@H](C(....
27 5C7C ic50 = 5.5 uM 4YC C17 H25 Cl N3 O C[C@@H]1CN....
28 3UW4 Ki = 0.017 uM MAA CHG PRO 0DQ n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: X23; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 X23 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3CM2; Ligand: X23; Similar sites found: 48
This union binding pocket(no: 1) in the query (biounit: 3cm2.bio8) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1S4M LUM 0.008142 0.43688 None
2 3GZ8 APR 0.009062 0.42667 None
3 1VG8 GNP 0.02019 0.41471 None
4 1H6H PIB 0.00652 0.41145 None
5 5L83 ASP TRP GLU ILE VAL 0.0004828 0.43423 1.78571
6 5F6U 5VK 0.00012 0.50296 2.30769
7 2RHO GSP 0.00986 0.42959 2.46154
8 5XDT MB3 0.04794 0.4029 2.5974
9 5FUI APY 0.0001124 0.52482 3.07692
10 3KYF 5GP 5GP 0.002409 0.41401 3.07692
11 2RDE C2E 0.002743 0.44053 3.84615
12 1SSQ CYS 0.02204 0.41784 3.84615
13 3A5Y KAA 0.02537 0.40663 3.84615
14 2X4Z X4Z 0.009501 0.44099 4.61538
15 4N14 WR7 0.006195 0.41202 4.61538
16 3A5Z KAA 0.03348 0.40309 4.61538
17 1G51 AMO 0.03898 0.40088 4.61538
18 3ACL 3F1 0.006086 0.42784 5.38462
19 1HXD BTN 0.01422 0.41123 5.38462
20 2WZ5 MET 0.00006808 0.4155 6.15385
21 1M15 ADP 0.04772 0.40301 6.15385
22 1M15 ARG 0.04772 0.40301 6.15385
23 1N07 FMN 0.01791 0.42502 6.92308
24 12AS AMP 0.01795 0.41877 6.92308
25 4DQ2 BTX 0.02174 0.41694 6.92308
26 5H06 MAL 0.01395 0.40366 6.92308
27 2G30 ALA ALA PHE 0.00008576 0.45141 7.69231
28 1BC5 ACE ASN TRP GLU THR PHE 0.002217 0.43974 7.69231
29 1NFS DED 0.01001 0.41696 7.69231
30 1RYA GDP 0.02464 0.41014 7.69231
31 4M1U MBG A2G 0.0114 0.42478 8.46154
32 5C5H 4YB 0.02792 0.40727 8.46154
33 5KJW 53C 0.0004861 0.47455 9.23077
34 3IES M24 0.006476 0.4511 9.23077
35 3A7R LAQ 0.03021 0.41593 9.23077
36 1GPM AMP 0.00602 0.41828 10
37 4DS0 A2G GAL NAG FUC 0.001171 0.44279 11.5385
38 1X54 4AD 0.02166 0.41169 11.5385
39 1Q0S SAH 0.03244 0.40245 11.5385
40 3IWD M2T 0.004453 0.42968 11.7647
41 1IID NHM 0.02477 0.42452 13.0769
42 2YNC YNC 0.03318 0.4137 13.0769
43 3OV6 MK0 0.03789 0.40518 13.8462
44 1ORR NAD 0.01946 0.4242 16.1538
45 5DX0 SFG 0.02462 0.41016 16.1538
46 5ALC TIQ 0.007459 0.44028 20.7692
47 1MWH GTG 0.01398 0.40537 22.3077
48 3UEC ALA ARG TPO LYS 0.0000003039 0.64844 33.0769
Pocket No.: 2; Query (leader) PDB : 3CM2; Ligand: X23; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3cm2.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3CM2; Ligand: X23; Similar sites found: 12
This union binding pocket(no: 3) in the query (biounit: 3cm2.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4L3L 5FI 0.02032 0.42143 None
2 4J6W CTP 0.03916 0.40647 None
3 4DE9 VTP 0.03494 0.40893 4.61538
4 4IGQ THR M3L GLN 0.007617 0.43064 6.15385
5 4CFP NAG AMU NAG AMV 0.03718 0.40223 7.69231
6 5J8O 6GZ 0.02019 0.4046 8.06452
7 5J75 6GQ 0.007836 0.42301 9.23077
8 1NB9 RBF 0.0262 0.42332 10
9 1NB9 ADP 0.0262 0.42332 10
10 2ZKJ ADP 0.02815 0.42332 13.0769
11 4DSU BZI 0.01027 0.40304 13.8462
12 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU 0.0002158 0.41125 31.5789
Pocket No.: 4; Query (leader) PDB : 3CM2; Ligand: X23; Similar sites found: 10
This union binding pocket(no: 4) in the query (biounit: 3cm2.bio10) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1VPD TLA 0.01069 0.40704 1.53846
2 4XUC 43G 0.01167 0.43921 3.84615
3 4XUC SAM 0.01167 0.43921 3.84615
4 3EFS BTN 0.01682 0.41267 3.86266
5 2XVD AS6 0.02998 0.40975 4.61538
6 3ZNR NU9 0.02506 0.40206 4.61538
7 4PIV NDP 0.03686 0.40469 6.15385
8 3DUW SAH 0.02803 0.40243 6.15385
9 2C91 NAP 0.04445 0.40731 11.5385
10 1FIQ FAD 0.04477 0.40669 14.6154
Pocket No.: 5; Query (leader) PDB : 3CM2; Ligand: X23; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 3cm2.bio3) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3CM2; Ligand: X23; Similar sites found: 5
This union binding pocket(no: 6) in the query (biounit: 3cm2.bio3) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4NS0 PIO 0.01263 0.40917 None
2 4HVA 4HV 0.03653 0.40365 1.53846
3 4HWT 1B2 0.02006 0.40544 3.07692
4 4GK9 MAN BMA MAN MAN MAN 0.0078 0.40461 6.92308
5 3RYC GTP 0.0153 0.42754 13.8462
Pocket No.: 7; Query (leader) PDB : 3CM2; Ligand: X23; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 3cm2.bio5) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 3CM2; Ligand: X23; 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: 3cm2.bio5) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 3CM2; Ligand: X23; Similar sites found: 18
This union binding pocket(no: 9) in the query (biounit: 3cm2.bio7) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3E5H GNP 0.008571 0.43665 None
2 2UZH CDP 0.0227 0.40265 None
3 4C2X NHW 0.0317 0.42057 1.53846
4 2PD4 DCN 0.04222 0.40862 2.30769
5 2PD4 NAD 0.04414 0.40765 2.30769
6 2WDB NAG MAN 0.007864 0.42693 3.07692
7 3FJO FAD 0.02396 0.40176 3.07692
8 1OIX GDP 0.03411 0.40317 3.84615
9 4KVG GTP 0.0297 0.4066 4.61538
10 3VEH 0GA 0.02268 0.40053 4.61538
11 3UWV 2PG 0.01792 0.41343 5.38462
12 5EKO N17 0.02015 0.41163 5.38462
13 1KBI PYR 0.03226 0.40743 6.92308
14 1LDN NAD 0.04062 0.40637 7.69231
15 3P3G UKW 0.02709 0.41168 9.23077
16 3P3G 3P3 0.02709 0.41168 9.23077
17 1ZC3 GNP 0.03077 0.40731 15.3846
18 3IQE F42 0.04748 0.40319 19.2308
Pocket No.: 10; Query (leader) PDB : 3CM2; Ligand: X23; Similar sites found: 11
This union binding pocket(no: 10) in the query (biounit: 3cm2.bio14) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2VG1 FPP 0.03519 0.40215 5.38462
2 2C4I BTN 0.02338 0.40066 5.38462
3 5F3I 5UJ 0.04488 0.40067 7.69231
4 2D1S SLU 0.02723 0.41443 8.46154
5 5LRT ADP 0.03812 0.40174 8.46154
6 5UIU 8CG 0.04609 0.40082 9.23077
7 4CS4 AXZ 0.02896 0.42505 10.7692
8 4CS4 ANP 0.0245 0.42421 10.7692
9 5L2J 6UL 0.0291 0.43825 18.3673
10 5L2J 70E 0.03045 0.43825 18.3673
11 2VAP GDP 0.01015 0.43653 19.2308
Pocket No.: 11; Query (leader) PDB : 3CM2; Ligand: X23; Similar sites found: 10
This union binding pocket(no: 11) in the query (biounit: 3cm2.bio15) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3F5O UOC COA 0.04064 0.40242 None
2 2J7T 274 0.04879 0.40007 3.07692
3 3ZF8 GDP 0.0193 0.4005 4.61538
4 3H4L ANP 0.03106 0.40339 5.38462
5 3EHH ADP 0.01071 0.4112 6.15385
6 4XV1 904 0.03017 0.41368 7.69231
7 2QTZ FAD 0.02214 0.40502 8.46154
8 2VNF ALA ARG THR M3L GLN THR ALA ARG LYS SER 0.02271 0.40631 10
9 3CZ7 ACO 0.03399 0.40322 13.0769
10 4G4P GLN 0.01145 0.4051 16.1538
Pocket No.: 12; Query (leader) PDB : 3CM2; Ligand: X23; Similar sites found: 3
This union binding pocket(no: 12) in the query (biounit: 3cm2.bio9) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3VC3 C6P 0.03948 0.40004 5.38462
2 4I54 1C1 0.03704 0.41124 8.46154
3 4YEF 4CQ 0.03549 0.41081 15.7303
Pocket No.: 13; Query (leader) PDB : 3CM2; Ligand: X23; Similar sites found: 5
This union binding pocket(no: 13) in the query (biounit: 3cm2.bio12) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3QXV MTX 0.02559 0.40124 3.96825
2 3LF0 ATP 0.03684 0.4015 5.26316
3 5UKL SIX 0.03506 0.40229 5.38462
4 1TPY SAH 0.03438 0.40128 9.23077
5 1NLU IVA PHI TYB 0.01873 0.40206 29.2308
Pocket No.: 14; Query (leader) PDB : 3CM2; Ligand: X23; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 14) in the query (biounit: 3cm2.bio2) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 15; Query (leader) PDB : 3CM2; Ligand: X23; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 15) in the query (biounit: 3cm2.bio2) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 16; Query (leader) PDB : 3CM2; Ligand: X23; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 16) in the query (biounit: 3cm2.bio4) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 17; Query (leader) PDB : 3CM2; Ligand: X23; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 17) in the query (biounit: 3cm2.bio4) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 18; Query (leader) PDB : 3CM2; Ligand: X23; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 18) in the query (biounit: 3cm2.bio13) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 19; Query (leader) PDB : 3CM2; Ligand: X23; Similar sites found: 2
This union binding pocket(no: 19) in the query (biounit: 3cm2.bio11) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4FC7 COA 0.03837 0.41757 6.92308
2 4FC7 NAP 0.03837 0.41757 6.92308
Pocket No.: 20; Query (leader) PDB : 3CM2; Ligand: X23; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 20) in the query (biounit: 3cm2.bio6) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback