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Receptor
PDB id Resolution Class Description Source Keywords
3G4Q 1.6 Å NON-ENZYME: TRANSPORT LIGAND MIGRATION AND CAVITIES WITHIN SCAPHARCA DIMERIC HEMOGLOBIN: WILD TYPE WITH CO BOUND TO HEME AND CHLOROFORM B OUND TO THE XE4 CAVITY SCAPHARCA INAEQUIVALVIS OXYGEN TRANSPORT ALLOSTERY OXYGEN AFFINITY CYTOPLASM HEME IRON METAL-BINDING OXYGEN STORAGE/TRANSPORT OXYGENBINDING TRANSPORT
Ref.: LIGAND MIGRATION AND CAVITIES WITHIN SCAPHARCA DIMERIC HBI: STUDIES BY TIME-RESOLVED CRYSTALLO-GRAPHY, XE BINDING, AND COMPUTATIONAL ANALYSIS. STRUCTURE V. 17 1494 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CMO A:148;
B:148;
Invalid;
Invalid;
none;
none;
submit data
28.01 C O [C-]#...
HEM A:147;
B:147;
Part of Protein;
Part of Protein;
none;
none;
submit data
616.487 C34 H32 Fe N4 O4 Cc1c2...
MCH A:151;
B:150;
B:152;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
119.378 C H Cl3 C(Cl)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3G4Q 1.6 Å NON-ENZYME: TRANSPORT LIGAND MIGRATION AND CAVITIES WITHIN SCAPHARCA DIMERIC HEMOGLOBIN: WILD TYPE WITH CO BOUND TO HEME AND CHLOROFORM B OUND TO THE XE4 CAVITY SCAPHARCA INAEQUIVALVIS OXYGEN TRANSPORT ALLOSTERY OXYGEN AFFINITY CYTOPLASM HEME IRON METAL-BINDING OXYGEN STORAGE/TRANSPORT OXYGENBINDING TRANSPORT
Ref.: LIGAND MIGRATION AND CAVITIES WITHIN SCAPHARCA DIMERIC HBI: STUDIES BY TIME-RESOLVED CRYSTALLO-GRAPHY, XE BINDING, AND COMPUTATIONAL ANALYSIS. STRUCTURE V. 17 1494 2009
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 3G4W - 8CL C6 H5 Cl c1ccc(cc1)....
2 3G4V - 7CL C5 H11 Cl CCCCCCl
3 3G4U - 0CL C3 H6 Cl2 C(CCl)CCl
4 3G52 - CEE C8 H9 Cl c1ccc(cc1)....
5 3G4Y - 9CL C7 H7 Cl c1ccc(cc1)....
6 3G4Q - MCH C H Cl3 C(Cl)(Cl)C....
7 3G53 - LT1 C9 H11 Cl c1ccc(cc1)....
8 3G4R - DCE C2 H4 Cl2 C(CCl)Cl
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 175 families.
1 3G4W - 8CL C6 H5 Cl c1ccc(cc1)....
2 3G4V - 7CL C5 H11 Cl CCCCCCl
3 3G4U - 0CL C3 H6 Cl2 C(CCl)CCl
4 3G52 - CEE C8 H9 Cl c1ccc(cc1)....
5 3G4Y - 9CL C7 H7 Cl c1ccc(cc1)....
6 3G4Q - MCH C H Cl3 C(Cl)(Cl)C....
7 3G53 - LT1 C9 H11 Cl c1ccc(cc1)....
8 3G4R - DCE C2 H4 Cl2 C(CCl)Cl
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 149 families.
1 3G4W - 8CL C6 H5 Cl c1ccc(cc1)....
2 3G4V - 7CL C5 H11 Cl CCCCCCl
3 3G4U - 0CL C3 H6 Cl2 C(CCl)CCl
4 3G52 - CEE C8 H9 Cl c1ccc(cc1)....
5 3G4Y - 9CL C7 H7 Cl c1ccc(cc1)....
6 3G4Q - MCH C H Cl3 C(Cl)(Cl)C....
7 3G53 - LT1 C9 H11 Cl c1ccc(cc1)....
8 3G4R - DCE C2 H4 Cl2 C(CCl)Cl
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MCH; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 MCH 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3G4Q; Ligand: MCH; Similar sites found with APoc: 93
This union binding pocket(no: 1) in the query (biounit: 3g4q.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4INB 1F6 None
2 4RJD TFP None
3 3T4L ZEA None
4 4MUV PCG None
5 3COW 52H None
6 2A1L PCW None
7 3E3U NVC None
8 1PZL MYR 1.36986
9 2YFB SIN 2.05479
10 4C3Y ANB 2.05479
11 4C3Y FAD 2.05479
12 2QZT PLM 2.7027
13 5C1M OLC 2.73973
14 5HSA FAS 3.42466
15 3V1S 0LH 3.42466
16 5LGA 6VH 3.42466
17 4O4K 2PK 3.42466
18 1ZDT PEF 3.42466
19 4WQ2 3SU 3.42466
20 5LWY OLB 3.42466
21 1HV9 UD1 4.10959
22 5AZC PGT 4.10959
23 3IPQ 965 4.10959
24 5F2K OCA 4.10959
25 5F2K SAH 4.10959
26 5KOD IAC 4.79452
27 2QZO KN1 4.79452
28 2QE4 JJ3 4.79452
29 4WGF HX2 4.79452
30 5AAV GW5 4.79452
31 2BJ4 OHT 4.79452
32 1LTT GAL BGC 4.79452
33 5Z1N PEF 4.79452
34 1LT3 GAL BGC 4.79452
35 4MG7 27H 4.79452
36 3KO0 TFP 4.9505
37 5UWA 8ND 5.47945
38 4QWT ACD 5.47945
39 5OSW AE4 5.47945
40 4M8E 29V 5.47945
41 4POJ 2VP 5.47945
42 4ZBR NPS 6.16438
43 4ZBR DIF 6.16438
44 2I0G I0G 6.16438
45 1U3R 338 6.16438
46 1XVB BHL 6.16438
47 5CSD ACD 6.16438
48 6H3O FAD 6.16438
49 2CDC XYS 6.16438
50 1LTI GAL 6.25
51 6BVM EBV 6.84932
52 6BVK EAV 6.84932
53 4URX FK1 6.84932
54 6BVJ EAS 6.84932
55 5UC1 486 6.84932
56 6BVL EBY 6.84932
57 5AG3 3EB 6.84932
58 6BVI EC4 6.84932
59 2E2R 2OH 7.53425
60 4GNI ATP 7.53425
61 6MPT C30 7.53425
62 5O4F 8VE 7.53425
63 2Z77 HE7 7.91367
64 1FM9 9CR 8.21918
65 2PD4 DCN 8.21918
66 2PD4 NAD 8.21918
67 3OJF IMJ 8.21918
68 3OJF NDP 8.21918
69 1RDT L79 8.21918
70 2Z7I 742 8.90411
71 3V49 PK0 8.90411
72 1T3Q MCN 8.90411
73 2IYA ZIO 10.274
74 1P7T PYR 10.9589
75 5ITZ GTP 11.6438
76 3RYC GTP 11.6438
77 5HCV 60R 13.0137
78 5L7G 6QE 13.0137
79 4UDB CV7 13.0137
80 1OLM VTQ 13.6986
81 4P6X HCY 15.0685
82 4OAR 2S0 15.0685
83 3RY9 1CA 15.0685
84 1SR7 MOF 15.0685
85 4BKS X6C 15.4639
86 4W9F 3JU 15.4639
87 3HRD FAD 15.7534
88 6H8S FSZ 16.4384
89 5HM3 649 17.1233
90 6ADI 9UO 17.1233
91 5Z84 CHD 21.2766
92 5ZCO CHD 21.2766
93 5EIB GTP 30.4348
Pocket No.: 2; Query (leader) PDB : 3G4Q; Ligand: MCH; Similar sites found with APoc: 139
This union binding pocket(no: 2) in the query (biounit: 3g4q.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 3ZLR X0B None
2 5O2D 9HH None
3 2AG5 NAD None
4 2GTE VA None
5 5DLY SAH None
6 1LRI CLR None
7 1MJH ATP None
8 1EJB INJ None
9 3SE5 ANP None
10 3LXI CAM None
11 3ZLM ANP None
12 5IF4 6AK None
13 1GZ6 NAI 2.05479
14 1VQ2 DDN 2.05479
15 4BNU 9KQ 2.05479
16 1TB3 FMN 2.05479
17 2DX7 CIT 2.05479
18 2VBQ BSJ 2.73973
19 1F9A ATP 2.73973
20 3UDZ ADP 2.73973
21 3GYT DL4 2.73973
22 4EN4 ATP 3.42466
23 4EN4 GT0 3.42466
24 4EN4 GT1 3.42466
25 2EWM NAD 3.42466
26 5WP4 PC 3.42466
27 2Q2V NAD 3.42466
28 1ST0 GTG 3.42466
29 3BXF 13P 3.42466
30 3KXC PLM 3.42466
31 3A28 NAD 3.42466
32 1IY8 NAD 4.10959
33 1RJW ETF 4.10959
34 3GUZ PAF 4.10959
35 1K6M AGS 4.10959
36 4UNR QZE 4.10959
37 6C7D EOJ 4.10959
38 5HR5 ADP 4.10959
39 4QOM PYG 4.10959
40 4C5N PXL 4.79452
41 2R40 20E 4.79452
42 5JWC 4W0 4.79452
43 2QA8 GEN 4.79452
44 1I2L DCS 4.79452
45 4X7Q 3YR 4.79452
46 1P0F NAP 4.79452
47 2ZCQ B65 4.79452
48 4C5N ACP 4.79452
49 1BUC CAA 4.79452
50 1JQI CAA 4.79452
51 5HYR EST 4.79452
52 5DXG EST 4.79452
53 4K4D HFQ 5.10949
54 5BYK OAQ 5.47945
55 5BYK A3P 5.47945
56 3E8N VRA 5.47945
57 3E8N ATP 5.47945
58 1KPH 10A 5.47945
59 2OZ5 7XY 5.47945
60 3CB2 GDP 5.47945
61 5K8C NAD 5.47945
62 2BTO GTP 5.47945
63 1Z6Z NAP 5.47945
64 6GG9 FMN 6.16438
65 4C0C WVH 6.16438
66 3KP6 SAL 6.16438
67 4YDU ADP 6.16438
68 5KBZ 3B2 6.16438
69 4XF6 ADP 6.16438
70 4XF6 LIP 6.16438
71 4XF6 INS 6.16438
72 4EUU BX7 6.16438
73 4D52 GXL 6.16438
74 5OC1 FAD 6.16438
75 4IZC 1GZ 6.16438
76 2F7A BEZ 6.16438
77 3CTL S6P 6.16438
78 3ZS7 ATP 6.84932
79 1GNI OLA 6.84932
80 2CFC NAD 6.84932
81 2O4J VD4 6.84932
82 1RM6 PCD 6.84932
83 4XU6 TDA 6.84932
84 5N7O 69Y 6.84932
85 6FCX SAH 6.84932
86 2HFN FMN 6.84932
87 2HVW DDN 6.84932
88 3FV3 IVA VAL VAL STA ALA STA 7.53425
89 5APK 76E 7.53425
90 2VL8 UDP 7.53425
91 1FFU FAD 8.21918
92 4F2Q QUS 8.21918
93 5N5U 7N8 8.21918
94 5Z2L NDP 8.21918
95 3H0A D30 8.21918
96 5CYV WCA 8.90411
97 4Z24 FAD 8.90411
98 2YPO PHE 8.90411
99 5DRB 5FJ 9.58904
100 2WUF KEM 9.58904
101 2X3F APC 9.58904
102 3H78 BE2 9.58904
103 5IDM ANP 9.58904
104 4ZOH FAD 10.274
105 5EK3 5PK 10.274
106 3CH6 NAP 10.274
107 3CH6 311 10.274
108 4B2Z P5S 10.274
109 4XRZ SI6 10.274
110 1ZBQ NAD 10.9589
111 5CMK GLU 10.9589
112 5IQT 6CU 10.9589
113 5IQT AKG 10.9589
114 3RYC GDP 11.6438
115 4CQM NAP 11.6438
116 2XRH NIO 12
117 4Z87 5GP 12.3288
118 3G6K POP 12.3288
119 3G6K FAD 12.3288
120 1D1T NAD 12.3288
121 5V03 658 12.7451
122 2F1K NAP 13.6986
123 4W6Z 8ID 15.0685
124 1PZO CBT 15.0685
125 2X5F PLP 15.0685
126 4B9K TG0 15.4639
127 5NVX 4YY 15.4639
128 4W9H 3JF 15.4639
129 3HRD MCN 15.7534
130 3A51 VDY 16.4384
131 1OE0 TTP 17.1233
132 1S7N COA 17.8082
133 2ZAT NAP 18.4932
134 4RFM 3P6 19.863
135 2DYS TGL 21.2766
136 2DYS PGV 21.2766
137 5Z84 PGV 21.2766
138 2DYR PGV 21.2766
139 1VL8 NAP 22.6027
Pocket No.: 3; Query (leader) PDB : 3G4Q; Ligand: MCH; Similar sites found with APoc: 62
This union binding pocket(no: 3) in the query (biounit: 3g4q.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 3NJQ NJQ None
2 6D6L FY4 None
3 6BXL SAM None
4 5X8I SQZ None
5 2C94 TSF 1.36986
6 1G2N EPH 2.73973
7 3QP8 HL0 2.73973
8 2D8L UCD 2.73973
9 2BIF ANP 2.73973
10 3AAQ ARU 2.73973
11 1C3Q TZE 3.16901
12 2DKN NAI 3.42466
13 5E7V M7E 3.42466
14 2OBD 2OB 3.42466
15 1TMM HHR 3.42466
16 1TMM APC 3.42466
17 4K26 NDP 3.42466
18 4JKV 1KS 3.42466
19 1E3W NAD 4.10959
20 1E6W NAD 4.10959
21 1U3U BNF 4.10959
22 1U3U NAD 4.10959
23 5LLT DND 4.10959
24 4GID 0GH 4.79452
25 5HWO HMG 4.79452
26 4I42 1HA 4.79452
27 1F74 NAY 4.79452
28 1RKD RIB 4.79452
29 1RKD ADP 4.79452
30 5VSM MET 4.79452
31 1KZN CBN 5.47945
32 1MLY ACZ PLP 5.47945
33 1KPG 16A 5.47945
34 2VK4 TPP 5.47945
35 5Y0T TAT 5.47945
36 6AM8 PLT 5.47945
37 1U7T NAD 6.16438
38 4L1F COS 6.16438
39 3EYA TDP 6.16438
40 4ITH RCM 6.16438
41 2X6T NAP 6.16438
42 4BQH 9VU 6.84932
43 1A59 COA 6.84932
44 1EDO NAP 6.84932
45 3SUD SUE 6.84932
46 5L92 C0R 6.84932
47 3ZRM ZRM 7.53425
48 1NP7 FAD 8.90411
49 2YC5 6BC 9.58904
50 4XB4 45D 10.274
51 1EWF PC1 10.9589
52 2QCS ANP 10.9589
53 3VRY B43 12.3288
54 5ZYN FAD 15.7534
55 1YIQ PQQ 18.4932
56 5ZCO TGL 21.2766
57 5ZCO PGV 21.2766
58 5Z84 PSC 21.2766
59 5ZCO PSC 21.2766
60 4R5M NAP 22.6027
61 4R5M 4NO 22.6027
62 5GWT NAD 28.0822
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