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Receptor
PDB id Resolution Class Description Source Keywords
3ILR 1.5 Å EC: 4.2.2.7 STRUCTURE OF HEPARINASE I FROM BACTEROIDES THETAIOTAOMICRON WITH TETRASACCHARIDE PRODUCT BACTEROIDES THETAIOTAOMICRON HEPARIN POLYSACCHARIDE LYASE BETA-JELLY ROLL LYASE
Ref.: STRUCTURAL SNAPSHOTS OF HEPARIN DEPOLYMERIZATION BY LYASE I. J.BIOL.CHEM. V. 284 34019 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:1;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
EDO A:3;
A:380;
A:381;
A:4;
A:5;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
IXD A:379;
Valid;
none;
submit data
256.187 C6 H8 O9 S C1=C(...
SGN A:378;
Valid;
none;
submit data
339.298 C6 H13 N O11 S2 C([C@...
SGN IXD A:377;
Valid;
none;
submit data
575.454 n/a S(=O)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3ILR 1.5 Å EC: 4.2.2.7 STRUCTURE OF HEPARINASE I FROM BACTEROIDES THETAIOTAOMICRON WITH TETRASACCHARIDE PRODUCT BACTEROIDES THETAIOTAOMICRON HEPARIN POLYSACCHARIDE LYASE BETA-JELLY ROLL LYASE
Ref.: STRUCTURAL SNAPSHOTS OF HEPARIN DEPOLYMERIZATION BY LYASE I. J.BIOL.CHEM. V. 284 34019 2009
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3INA - IDS SGN IDS SGN IDS SUS IDS SGN n/a n/a
2 3IN9 - H1S C12 H15 N O19 S3 C1=C(O[C@H....
3 3ILR - IXD C6 H8 O9 S C1=C(O[C@H....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3INA - IDS SGN IDS SGN IDS SUS IDS SGN n/a n/a
2 3IN9 - H1S C12 H15 N O19 S3 C1=C(O[C@H....
3 3ILR - IXD C6 H8 O9 S C1=C(O[C@H....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3INA - IDS SGN IDS SGN IDS SUS IDS SGN n/a n/a
2 3IN9 - H1S C12 H15 N O19 S3 C1=C(O[C@H....
3 3ILR - IXD C6 H8 O9 S C1=C(O[C@H....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: IXD; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 IXD 1 1
Ligand no: 2; Ligand: SGN; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 YJM 1 1
2 SGN 1 1
3 NGS 0.603774 0.870968
4 3LJ 0.5 0.898305
Ligand no: 3; Ligand: SGN IXD; Similar ligands found: 14
No: Ligand ECFP6 Tc MDL keys Tc
1 IDU SGN 1 1
2 SGN IXD 1 1
3 IDS SGN IDS SGN IDS 0.627451 0.984127
4 H1S 0.588889 0.953125
5 SGN IDS SGN IDS 0.539216 0.968254
6 SGN IDS SGN IDS SGN 0.537037 0.96875
7 IDS SGN IDS SGN IDS IDS 0.504505 0.96875
8 UAP SGN IDS SGN IDS SGN 0.5 0.938462
9 UAP SGN IDS SGN 0.5 0.938462
10 SGN IDS UAP SGN 0.5 0.938462
11 SGN IDS UAP SGN IDS SGN 0.5 0.938462
12 SGN IDS SGN IDS SGN IDS 0.439655 0.96875
13 H3S 0.43299 0.938462
14 ASG GCD 0.414141 0.850746
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3ILR; Ligand: IXD; Similar sites found with APoc: 111
This union binding pocket(no: 1) in the query (biounit: 3ilr.bio1) has 46 residues
No: Leader PDB Ligand Sequence Similarity
1 5I35 ANP 1.35135
2 4I9A NCN 1.38889
3 3B8Y ADA ADA ADA ADA 1.45349
4 4D4U FUC NDG GAL FUC 1.5873
5 5UQD AKG 1.62162
6 6BMN PAP 1.69492
7 2PYW ADP 1.89189
8 3EPO MP5 1.89189
9 2F57 23D 1.89274
10 4FFG 0U8 2.16216
11 5A2B MAL 2.16216
12 4X7Q 3YR 2.24359
13 4RD0 GDP 2.43243
14 2CYB TYR 2.47678
15 5HCA BGC 2.55474
16 2RG0 CBI 2.7027
17 2QK4 ATP 2.87611
18 1JPA ANP 2.88462
19 4AVV CD 2.94118
20 3ZGJ RMN 2.97297
21 2PUL ACP 2.97297
22 2IFB PLM 3.05344
23 5W75 SUC 3.24324
24 1LSH PLD 3.24324
25 1ZM1 BGC BGC BGC 3.3195
26 4KBA 1QM 3.51351
27 4UX9 ANP 3.57143
28 3NV3 GAL NAG MAN 3.62319
29 3HAV ATP 3.67893
30 1IS3 LAT 3.7037
31 3WV6 GAL GLC 3.71622
32 3WV6 GAL BGC 3.71622
33 1WKM MET 3.72881
34 3VV1 GAL FUC 3.75
35 1DZT TPE 3.82514
36 4Y85 499 3.91566
37 3TXO 07U 3.96601
38 5DO8 BGC 4.05405
39 4ZU4 4TG 4.05405
40 1Y2F WAI 4.31655
41 2P7Q GG6 4.51128
42 3A76 SPD 4.54545
43 6AC9 ANP 4.59459
44 1SZ0 M6P 4.59459
45 5YF9 NIO 4.59459
46 5Y86 HRM 4.59459
47 5YIF 8VR 4.59459
48 6CED EYA 4.6729
49 5M06 ADP 4.86486
50 4TR9 38D 4.87805
51 6F5W KG1 4.87805
52 1U5R ATP 4.88506
53 5H9P TD2 5.06329
54 5L8L ADP 5.12821
55 6C0B MLI 5.13514
56 3WDX BGC BGC GLC 5.36913
57 3WDX BGC BGC BGC 5.36913
58 1UMZ BGC BGC XYS BGC XYS GAL 5.39568
59 2ZHL NAG GAL GAL NAG 5.40541
60 4ZU5 THM 5.55556
61 3QDV NDG 5.59441
62 5TPV TYD 5.67568
63 5UMY TNN 5.71429
64 5DG2 GAL GLC 5.92593
65 5W0N UPU 5.94595
66 2ET1 GLV 5.97015
67 1OGX EQU 6.10687
68 3WG3 A2G GAL NAG FUC 6.17978
69 5KEW 6SB 6.38298
70 5FU3 BGC BGC BGC 6.60377
71 2BS5 BGC GAL FUC 6.66667
72 2BMB PMM 6.75676
73 3ZXE PGZ 6.76692
74 1WW5 SGA BGC 6.875
75 4L4J NAG NAG BMA MAN NAG 7.23982
76 5OES ADP 7.2973
77 6F9G PUT 7.2973
78 5NW7 9C2 7.2973
79 5NFB 8VT 7.38636
80 2WQN ADP 7.41935
81 3M3E GAL A2G NPO 7.45342
82 4HSJ 6PC 7.47126
83 6GR0 F8W 7.47126
84 5ZCT ANP 7.51634
85 4RF7 ARG 7.83784
86 1A78 TDG 8.20895
87 1I7E IBS 8.30189
88 2R0H CTO 8.53659
89 4WOE ADP 8.64865
90 4XZ3 ACP 8.69565
91 1B09 PC 8.73786
92 3X01 AMP 9.72973
93 2HKA C3S 10
94 4YZT BGC BGC BGC BGC 10.2703
95 1QFT HSM 10.2857
96 4XYM A12 10.4348
97 4K55 H6P 10.4839
98 5GLT BGC GAL NAG GAL 11.2676
99 5FPX GLY SER SER HIS HIS HIS HIS HIS 12.3894
100 6ASZ GLN THR ALA ARG M3L SER 13.0435
101 3SAO NKN 13.125
102 5XQW 8EU 13.2701
103 1OGZ EQU 14.4
104 6FOF LAT 14.7959
105 5NCF 8T5 15.0442
106 5A65 TPP 15.2074
107 3ZW2 NAG GAL FUC 19.5402
108 6GNO XDI 20
109 2D6M LBT 20.1258
110 1C1L GAL BGC 23.3577
111 3RV5 DXC 23.5955
Pocket No.: 2; Query (leader) PDB : 3ILR; Ligand: SGN; Similar sites found with APoc: 111
This union binding pocket(no: 2) in the query (biounit: 3ilr.bio1) has 46 residues
No: Leader PDB Ligand Sequence Similarity
1 5I35 ANP 1.35135
2 4I9A NCN 1.38889
3 3B8Y ADA ADA ADA ADA 1.45349
4 4D4U FUC NDG GAL FUC 1.5873
5 5UQD AKG 1.62162
6 6BMN PAP 1.69492
7 2PYW ADP 1.89189
8 3EPO MP5 1.89189
9 2F57 23D 1.89274
10 4FFG 0U8 2.16216
11 5A2B MAL 2.16216
12 4X7Q 3YR 2.24359
13 4RD0 GDP 2.43243
14 2CYB TYR 2.47678
15 5HCA BGC 2.55474
16 2RG0 CBI 2.7027
17 2QK4 ATP 2.87611
18 1JPA ANP 2.88462
19 4AVV CD 2.94118
20 3ZGJ RMN 2.97297
21 2PUL ACP 2.97297
22 2IFB PLM 3.05344
23 5W75 SUC 3.24324
24 1LSH PLD 3.24324
25 1ZM1 BGC BGC BGC 3.3195
26 4KBA 1QM 3.51351
27 4UX9 ANP 3.57143
28 3NV3 GAL NAG MAN 3.62319
29 3HAV ATP 3.67893
30 1IS3 LAT 3.7037
31 3WV6 GAL GLC 3.71622
32 3WV6 GAL BGC 3.71622
33 1WKM MET 3.72881
34 3VV1 GAL FUC 3.75
35 1DZT TPE 3.82514
36 4Y85 499 3.91566
37 3TXO 07U 3.96601
38 5DO8 BGC 4.05405
39 4ZU4 4TG 4.05405
40 1Y2F WAI 4.31655
41 2P7Q GG6 4.51128
42 3A76 SPD 4.54545
43 6AC9 ANP 4.59459
44 1SZ0 M6P 4.59459
45 5YF9 NIO 4.59459
46 5Y86 HRM 4.59459
47 5YIF 8VR 4.59459
48 6CED EYA 4.6729
49 5M06 ADP 4.86486
50 4TR9 38D 4.87805
51 6F5W KG1 4.87805
52 1U5R ATP 4.88506
53 5H9P TD2 5.06329
54 5L8L ADP 5.12821
55 6C0B MLI 5.13514
56 3WDX BGC BGC GLC 5.36913
57 3WDX BGC BGC BGC 5.36913
58 1UMZ BGC BGC XYS BGC XYS GAL 5.39568
59 2ZHL NAG GAL GAL NAG 5.40541
60 4ZU5 THM 5.55556
61 3QDV NDG 5.59441
62 5TPV TYD 5.67568
63 5UMY TNN 5.71429
64 5DG2 GAL GLC 5.92593
65 5W0N UPU 5.94595
66 2ET1 GLV 5.97015
67 1OGX EQU 6.10687
68 3WG3 A2G GAL NAG FUC 6.17978
69 5KEW 6SB 6.38298
70 5FU3 BGC BGC BGC 6.60377
71 2BS5 BGC GAL FUC 6.66667
72 2BMB PMM 6.75676
73 3ZXE PGZ 6.76692
74 1WW5 SGA BGC 6.875
75 4L4J NAG NAG BMA MAN NAG 7.23982
76 5OES ADP 7.2973
77 6F9G PUT 7.2973
78 5NW7 9C2 7.2973
79 5NFB 8VT 7.38636
80 2WQN ADP 7.41935
81 3M3E GAL A2G NPO 7.45342
82 4HSJ 6PC 7.47126
83 6GR0 F8W 7.47126
84 5ZCT ANP 7.51634
85 4RF7 ARG 7.83784
86 1A78 TDG 8.20895
87 1I7E IBS 8.30189
88 2R0H CTO 8.53659
89 4WOE ADP 8.64865
90 4XZ3 ACP 8.69565
91 1B09 PC 8.73786
92 3X01 AMP 9.72973
93 2HKA C3S 10
94 4YZT BGC BGC BGC BGC 10.2703
95 1QFT HSM 10.2857
96 4XYM A12 10.4348
97 4K55 H6P 10.4839
98 5GLT BGC GAL NAG GAL 11.2676
99 5FPX GLY SER SER HIS HIS HIS HIS HIS 12.3894
100 6ASZ GLN THR ALA ARG M3L SER 13.0435
101 3SAO NKN 13.125
102 5XQW 8EU 13.2701
103 1OGZ EQU 14.4
104 6FOF LAT 14.7959
105 5NCF 8T5 15.0442
106 5A65 TPP 15.2074
107 3ZW2 NAG GAL FUC 19.5402
108 6GNO XDI 20
109 2D6M LBT 20.1258
110 1C1L GAL BGC 23.3577
111 3RV5 DXC 23.5955
Pocket No.: 3; Query (leader) PDB : 3ILR; Ligand: SGN IXD; Similar sites found with APoc: 124
This union binding pocket(no: 3) in the query (biounit: 3ilr.bio1) has 49 residues
No: Leader PDB Ligand Sequence Similarity
1 5I35 ANP 1.35135
2 4I9A NCN 1.38889
3 3B8Y ADA ADA ADA ADA 1.45349
4 4D4U FUC NDG GAL FUC 1.5873
5 1Q8Y ADE 1.62162
6 4RP9 ASC 1.89189
7 3EPO MP5 1.89189
8 1OFZ FUC 1.92308
9 4FFG 0U8 2.16216
10 5A2B MAL 2.16216
11 2FB3 5AD 2.35294
12 4RD0 GDP 2.43243
13 1Z3V LAT 2.43243
14 5X7Q GLC GLC GLC GLC 2.43243
15 4GK9 MAN BMA MAN MAN MAN 2.50896
16 5HCA BGC 2.55474
17 4KYS VIB 2.7027
18 2RFY CBI 2.7027
19 2RG0 CBI 2.7027
20 1U0A BGC BGC BGC BGC 2.80374
21 2QK4 ATP 2.87611
22 4AVV CD 2.94118
23 5AIG VPR 3.2
24 5W75 SUC 3.24324
25 1LSH PLD 3.24324
26 3H7J PPY 3.24324
27 4YLZ LAT NAG GAL 3.26797
28 5J75 6GQ 3.40909
29 4KBA 1QM 3.51351
30 1QKQ MAN 3.52113
31 4UX9 ANP 3.57143
32 1Y7P RIP 3.58744
33 3NV3 GAL NAG MAN 3.62319
34 1IS3 LAT 3.7037
35 3WV6 GAL GLC 3.71622
36 3WV6 GAL BGC 3.71622
37 1WKM MET 3.72881
38 3VV1 GAL FUC 3.75
39 2G50 ALA 3.78378
40 1SDW IYT 3.82166
41 1DZT TPE 3.82514
42 1SGJ OAA 3.87324
43 1F9V ADP 4.03458
44 4ZU4 4TG 4.05405
45 5DO8 BGC 4.05405
46 4WVW SLT 4.16667
47 5ODT ADP 4.24028
48 1Y2F WAI 4.31655
49 3FP0 FP0 4.32432
50 1SLT NDG GAL 4.47761
51 2P7Q GG6 4.51128
52 3A76 SPD 4.54545
53 1SZ0 M6P 4.59459
54 5YIF 8VR 4.59459
55 4HWT 1B2 4.59459
56 6CED EYA 4.6729
57 2VQ5 HBA 4.86486
58 3ZIA ADP 4.86486
59 5M06 ADP 4.86486
60 6F5W KG1 4.87805
61 1UPR 4IP 4.87805
62 1U5R ATP 4.88506
63 5H9P TD2 5.06329
64 6C0B MLI 5.13514
65 2HY0 306 5.2795
66 5D9G GLU ASN LEU TYR PHE GLN 5.28455
67 5FUI APY 5.30303
68 3WDX BGC BGC GLC 5.36913
69 3WDX BGC BGC BGC 5.36913
70 1UMZ BGC BGC XYS BGC XYS GAL 5.39568
71 1VMK GUN 5.40541
72 4ZU5 THM 5.55556
73 3E3U NVC 5.58376
74 5TPV TYD 5.67568
75 2YBP 2HG 5.67568
76 2Q8E OGA 5.96591
77 2ET1 GLV 5.97015
78 1ULE GLA GAL NAG 6
79 1OGX EQU 6.10687
80 5F6U 5VK 6.36943
81 5FU3 BGC BGC BGC 6.60377
82 6D61 4AA 6.66667
83 2BMB PMM 6.75676
84 1MZV AMP 6.80851
85 1WW5 SGA BGC 6.875
86 4L4J NAG NAG BMA MAN NAG 7.23982
87 5NW7 9C2 7.2973
88 5NFB 8VT 7.38636
89 2WQN ADP 7.41935
90 3M3E GAL A2G NPO 7.45342
91 4HSJ 6PC 7.47126
92 6GR0 F8W 7.47126
93 5ZCT ANP 7.51634
94 4IAW LIZ 7.97872
95 5L2R MLA 8.10811
96 2F6U CIT 8.11966
97 4XCB HY0 8.42912
98 4WOE ADP 8.64865
99 2YG2 S1P 8.72093
100 1B09 PC 8.73786
101 6CZI 38E 8.92857
102 2WMC MGP 8.98876
103 5ODY 9SK 9.42029
104 4MOB ADP 10.241
105 1QFT HSM 10.2857
106 4K55 H6P 10.4839
107 2V7Q ADP 10.6061
108 2BVE PH5 10.9244
109 5GLT BGC GAL NAG GAL 11.2676
110 4QPW XYP XYP XYP 11.2676
111 2XG5 EC2 12.1387
112 2XG5 EC5 12.1387
113 5DYO FLU 12.3853
114 6ASZ GLN THR ALA ARG M3L SER 13.0435
115 3SAO NKN 13.125
116 5XQW 8EU 13.2701
117 6FOF LAT 14.7959
118 3H0L ADP 17.2973
119 6GNO XDI 20
120 2D6M LBT 20.1258
121 3IWD M2T 20.9677
122 1C1L GAL BGC 23.3577
123 3RV5 DXC 23.5955
124 4M1U A2G MBG 27.1429
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