Receptor
PDB id Resolution Class Description Source Keywords
3LE7 1.65 Å EC: 3.2.2.22 CRYSTAL STRUCTURE OF PD-L1 FROM P. DIOICA IN COMPLEX WITH ADENINE PHYTOLACCA DIOICA RIBOSOME ADENINE DISULFIDE BOND GLYCOPROTEIN HYDROLASE PLANT DEFENSE PROTEIN SYNTHESIS INHIBITOR TOXIN
Ref.: THE ROLE OF THE GLYCAN MOIETY ON THE STRUCTURE-FUNCTION RELATIONSHIPS OF PD-L1, TYPE 1 RIBOSOME-INACTIVATING PROTEIN FROM P. DIOICA LEAVES MOL BIOSYST V. 6 570 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ADE A:501;
B:601;
Valid;
Valid;
none;
none;
submit data
135.127 C5 H5 N5 c1[nH...
NAG A:265;
A:3;
B:2;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3LE7 1.65 Å EC: 3.2.2.22 CRYSTAL STRUCTURE OF PD-L1 FROM P. DIOICA IN COMPLEX WITH ADENINE PHYTOLACCA DIOICA RIBOSOME ADENINE DISULFIDE BOND GLYCOPROTEIN HYDROLASE PLANT DEFENSE PROTEIN SYNTHESIS INHIBITOR TOXIN
Ref.: THE ROLE OF THE GLYCAN MOIETY ON THE STRUCTURE-FUNCTION RELATIONSHIPS OF PD-L1, TYPE 1 RIBOSOME-INACTIVATING PROTEIN FROM P. DIOICA LEAVES MOL BIOSYST V. 6 570 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 3LE7 - ADE C5 H5 N5 c1[nH]c2c(....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 2QES - ADE C5 H5 N5 c1[nH]c2c(....
2 2QET - ADE C5 H5 N5 c1[nH]c2c(....
3 1J1R - ADE C5 H5 N5 c1[nH]c2c(....
4 1J1S - FMP C10 H14 N5 O7 P c1nc2c(c(n....
5 1D6A - GUN C5 H5 N5 O c1[nH]c2c(....
6 1QCJ - APT C14 H13 N6 O3 c1cc(ccc1C....
7 1QCI - ADE C5 H5 N5 c1[nH]c2c(....
8 3LE7 - ADE C5 H5 N5 c1[nH]c2c(....
50% Homology Family (47)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5DDZ - ASP ASP ASP MET GLY PHE GLY LEU PHE ASP n/a n/a
2 4MX5 ic50 = 28 uM 5MX C17 H17 N7 O4 c1ccc(cc1)....
3 4HV7 ic50 = 300 uM 19J C11 H11 N7 O5 c1c(nc2c(n....
4 3PX8 ic50 = 230 uM JP2 C7 H5 N5 O3 c1c(nc2c(n....
5 5GU4 Kd = 3.4 uM ASP ASP MET GLY PHE GLY LEU PHE ASP n/a n/a
6 1BR6 Ki = 0.6 mM PT1 C14 H12 N6 O3 c1cc(ccc1C....
7 4ESI ic50 = 70 uM 0RB C10 H9 N9 O2 c1c([nH]nn....
8 4HV3 ic50 = 115 uM 19L C21 H20 N8 O6 c1ccc2c(c1....
9 1BR5 Ki = 2 mM NEO C9 H11 N5 O4 c1c(nc2c(n....
10 3EJ5 ic50 = 0.27 mM EJ5 C14 H15 N3 O4 c1cc(ccc1C....
11 4MX1 ic50 = 209 uM 1MX C16 H16 N8 O3 c1ccc(cc1)....
12 3PX9 ic50 = 380 uM JP3 C12 H10 N6 O3 c1cc(oc1)C....
13 4HUO ic50 = 20 uM RS8 C18 H17 N7 O5 c1ccc(cc1)....
14 2P8N Kd = 700 uM ADE C5 H5 N5 c1[nH]c2c(....
15 1J1M - TRE C12 H22 O11 C([C@@H]1[....
16 4Q2V - 0XE C21 H18 O11 c1ccc(cc1)....
17 4HUP ic50 = 15 uM 19M C27 H26 N8 O6 c1ccc(cc1)....
18 1IFS - ADE C5 H5 N5 c1[nH]c2c(....
19 1IFU - FMC C10 H13 N5 O4 c1nc2c(c(n....
20 3HIO - C2X C51 H72 N21 O29 P5 CO[C@@H]1[....
21 2PJO Kd = 900 mM NMU C2 H6 N2 O CNC(=O)N
22 2R3D Kd = 1.4 M ACM C2 H5 N O CC(=O)N
23 3KU0 - ADE C5 H5 N5 c1[nH]c2c(....
24 2QET - ADE C5 H5 N5 c1[nH]c2c(....
25 1LPC - CMP C10 H12 N5 O6 P c1nc(c2c(n....
26 1GIU - ADE C5 H5 N5 c1[nH]c2c(....
27 1MRK - FMC C10 H13 N5 O4 c1nc2c(c(n....
28 1QD2 - ADE C5 H5 N5 c1[nH]c2c(....
29 1TCS - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
30 1MRJ - ADN C10 H13 N5 O4 c1nc(c2c(n....
31 1NLI Kd = 260 uM ADE C5 H5 N5 c1[nH]c2c(....
32 1GIS - DA C10 H14 N5 O6 P c1nc(c2c(n....
33 1AHB - FMP C10 H14 N5 O7 P c1nc2c(c(n....
34 1AHA - ADE C5 H5 N5 c1[nH]c2c(....
35 3N1N - GUN C5 H5 N5 O c1[nH]c2c(....
36 3V2K - ADE C5 H5 N5 c1[nH]c2c(....
37 3RL9 - ADE C5 H5 N5 c1[nH]c2c(....
38 3SJ6 - RIP C5 H10 O5 C1[C@H]([C....
39 1MRH - FMC C10 H13 N5 O4 c1nc2c(c(n....
40 3U6Z - ADE C5 H5 N5 c1[nH]c2c(....
41 1MRG - ADN C10 H13 N5 O4 c1nc(c2c(n....
42 1J1S - FMP C10 H14 N5 O7 P c1nc2c(c(n....
43 1D6A - GUN C5 H5 N5 O c1[nH]c2c(....
44 1QCI - ADE C5 H5 N5 c1[nH]c2c(....
45 3LE7 - ADE C5 H5 N5 c1[nH]c2c(....
46 3HIW Ki = 3.9 nM C2X C51 H72 N21 O29 P5 CO[C@@H]1[....
47 3HIV Ki = 7.5 nM TXN C37 H52 N15 O20 P3 CO[C@@H]1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ADE; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 ADE 1 1
2 PM6 0.5 0.742857
3 ES4 0.463415 0.685714
4 6AP 0.428571 0.9375
5 XQG 0.422222 0.648649
6 M02 0.411765 0.630435
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3LE7; Ligand: ADE; Similar sites found: 103
This union binding pocket(no: 1) in the query (biounit: 3le7.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1XIU REA 0.02389 0.40337 None
2 1C9K 5GP 0.00407 0.43448 1.11111
3 1P9P SAH 0.01164 0.4235 1.14943
4 1PZG A3D 0.04077 0.41033 1.14943
5 2JG1 ANP 0.02675 0.40299 1.14943
6 1R6T TYM 0.03229 0.41849 1.53257
7 2XVD AS6 0.02583 0.41058 1.53257
8 1VJY 460 0.04263 0.40758 1.53257
9 3RDE OYP 0.02737 0.40399 1.53257
10 2Q4V ACO 0.01142 0.42981 1.76471
11 1YMT DR9 0.02917 0.40894 2.03252
12 3FAL REA 0.01978 0.4053 2.06612
13 1FBY REA 0.008148 0.43721 2.09205
14 1YP0 PEF 0.01631 0.41616 2.09205
15 4M8E 29V 0.02241 0.4097 2.1645
16 4POJ 2VP 0.02602 0.40769 2.1645
17 1QPG MAP 0.01741 0.42186 2.29885
18 1N6B DMZ 0.01151 0.41629 2.29885
19 1PGP 6PG 0.04874 0.40718 2.29885
20 4USF 6UI 0.0325 0.40146 2.29885
21 1M13 HYF 0.04887 0.40029 2.29885
22 1YOK P6L 0.0395 0.40749 2.34375
23 1ZDU P3A 0.01222 0.42689 2.44898
24 3ZS7 ATP 0.01638 0.4137 2.68199
25 4IVG ANP 0.02203 0.41207 2.68199
26 4M73 SAH 0.04809 0.40455 2.68199
27 4POW OP1 0.02725 0.40202 2.68199
28 1QZR ANP 0.01616 0.42323 3.06513
29 5EY0 GTP 0.01739 0.40225 3.06513
30 3OIG NAD 0.03736 0.40164 3.06513
31 2AX9 BHM 0.03086 0.42225 3.125
32 1YDK GTX 0.01825 0.42087 3.15315
33 1ZDT PEF 0.03598 0.40247 3.3195
34 2GJ3 FAD 0.01457 0.41437 3.33333
35 5C5H 4YB 0.0127 0.42437 3.44828
36 1PHP ADP 0.01557 0.42017 3.44828
37 4IA6 EIC 0.009626 0.40287 3.44828
38 1BKC INN 0.01645 0.40306 3.51562
39 2WTN FER 0.01541 0.40033 3.58566
40 2ZFZ ARG 0.03741 0.41818 3.79747
41 5VC5 96M 0.0127 0.42676 3.83142
42 2R40 20E 0.0128 0.42631 3.83142
43 1HXD BTN 0.01784 0.41373 3.83142
44 2QZO KN1 0.02719 0.40275 3.87597
45 4TUZ 36J 0.01109 0.41807 3.92157
46 4MGB XDH 0.01282 0.41575 3.92157
47 3FW4 CAQ 0.03949 0.40449 3.93258
48 1WG8 SAM 0.01215 0.42415 4.21456
49 1S4M LUM 0.02677 0.41126 4.21456
50 4KQI RBZ 0.03964 0.4058 4.21456
51 4KVL PLM 0.03197 0.40287 4.21456
52 3A51 VDY 0.01894 0.40221 4.21456
53 1ZGA HMK 0.006082 0.42239 4.5977
54 2RGJ FAD 0.03395 0.41592 4.5977
55 5MEX PAP 0.01685 0.41373 4.5977
56 5MEX SZZ 0.03964 0.41373 4.5977
57 4NTD FAD 0.03984 0.41246 4.5977
58 3NTA FAD 0.04919 0.40915 4.5977
59 2Y31 SMQ 0.03303 0.40756 4.5977
60 5TQZ GLC 0.002086 0.4228 4.66667
61 5IKB KAI 0.01499 0.40751 4.66926
62 3LCV SAM 0.01789 0.41479 4.98084
63 1QG6 NAD 0.03796 0.41472 4.98084
64 1QG6 TCL 0.03796 0.41472 4.98084
65 4LA7 A1O 0.03218 0.40726 4.98084
66 1FM9 9CR 0.0265 0.40462 4.98084
67 2ZYI STE 0.03288 0.40137 4.98084
68 1TMM HHR 0.006121 0.44445 5.06329
69 1TMM APC 0.006476 0.44445 5.06329
70 2ISJ FMN 0.03371 0.40198 5.21739
71 3SCM LGN 0.01143 0.45494 5.30612
72 5G3N X28 0.00652 0.43944 5.51181
73 3LZW FAD 0.04568 0.40834 5.74713
74 2HW1 ANP 0.02476 0.4031 5.74713
75 1X38 IDD 0.02812 0.40009 5.74713
76 1UOU CMU 0.004894 0.43468 6.13027
77 2C42 PYR 0.01117 0.43338 6.13027
78 1NV8 SAM 0.01412 0.42605 6.13027
79 1NV8 MEQ 0.01763 0.41897 6.13027
80 3ZLB ANP 0.01506 0.42193 6.51341
81 3FPF MTA 0.0286 0.42115 6.89655
82 3LDW IPE 0.02316 0.41351 6.89655
83 3LOO B4P 0.04539 0.40207 6.89655
84 2XTS MTE 0.01033 0.42523 7.27969
85 1RM6 FAD 0.0419 0.41255 7.45342
86 2QX0 APC 0.001778 0.44978 7.54717
87 1HN4 MJI 0.006847 0.47518 7.63359
88 2C9E PID 0.03099 0.40543 7.66284
89 2RC5 FAD 0.02293 0.40622 8.04598
90 1Y75 NAG 0.01333 0.40279 8.47458
91 5CSD ACD 0.02059 0.43057 8.80503
92 4MCC 21X 0.03089 0.4041 8.94309
93 2BII MTV 0.0106 0.42748 9.1954
94 1DKF OLA 0.02123 0.40223 9.78723
95 2X2M X2M 0.02707 0.40672 9.96169
96 1XNG DND 0.03748 0.40337 9.96169
97 1PZL MYR 0.01581 0.4117 10.5485
98 3FS1 MYR 0.02039 0.40423 10.8696
99 1D4D FAD 0.0249 0.42942 11.1111
100 3HUJ AGH 0.006245 0.4685 12.1212
101 2HKJ RDC 0.01473 0.42786 14.5594
102 2FYU FDN 0.01886 0.41037 15.3846
103 4WN5 MVC 0.02418 0.40578 18.2609
Pocket No.: 2; Query (leader) PDB : 3LE7; Ligand: ADE; Similar sites found: 31
This union binding pocket(no: 2) in the query (biounit: 3le7.bio2) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5K52 OCD 0.02738 0.40291 None
2 2IVD FAD 0.04929 0.40891 1.14943
3 4EN4 GT0 0.008787 0.44882 2.29885
4 4EN4 ATP 0.008787 0.44882 2.29885
5 4EN4 GT1 0.008787 0.44882 2.29885
6 2A9D MTE 0.01065 0.42273 2.29885
7 4C3Y FAD 0.04974 0.40788 2.29885
8 1QAN SAH 0.02785 0.40377 2.86885
9 5BUK FAD 0.0454 0.41605 3.06513
10 3DWB RDF 0.01773 0.40086 3.06513
11 1KRP DT DT PST 0.03857 0.4007 3.06513
12 1I1D COA 0.03159 0.40074 3.10559
13 2OO8 RAJ 0.02477 0.40424 3.44828
14 1V8B NAD 0.03756 0.41003 3.83142
15 1G2N EPH 0.03462 0.40154 3.83142
16 1VBO MAN MAN MAN 0.006625 0.40115 4.02685
17 2XVE FAD 0.04818 0.4215 4.21456
18 2WEI VGG 0.01715 0.40078 4.21456
19 1N4H REA 0.03613 0.40059 4.2471
20 2WYV NAD 0.02381 0.41812 4.5977
21 4DS8 A8S 0.02335 0.40084 4.98084
22 3G08 FEE 0.008238 0.46259 5.05051
23 3E8T UQ8 0.0465 0.42095 5.45455
24 1BRW URA 0.01081 0.40585 5.74713
25 5DT6 GLU 0.008881 0.40991 6.13027
26 3CGB FAD 0.04595 0.40423 6.51341
27 4CQM NAP 0.04011 0.40444 9.1954
28 1E3W NAD 0.04822 0.40157 9.96169
29 3NYQ MCA 0.04906 0.40199 11.1111
30 4FOJ C2E 0.01515 0.40787 11.8774
31 1YYE 196 0.01882 0.40386 15.7088
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