FAIRMol

Z20255081

Pose ID 11312 Compound 678 Pose 469

DB fairmolDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand Z20255081
PDB5S9T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
41.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.43, H-bond role recall 0.00
Burial
81%
Hydrophobic fit
65%
Reason: no major geometry red flags detected
1 protein-contact clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Daphnia EC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Algae IC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Risk
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.736 kcal/mol/HA) ✓ Good fit quality (FQ -7.10) ✓ Good H-bonds (4 bonds) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (65%) ✗ Extreme strain energy (41.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-22.083
kcal/mol
LE
-0.736
kcal/mol/HA
Fit Quality
-7.10
FQ (Leeson)
HAC
30
heavy atoms
MW
459
Da
LogP
4.59
cLogP
Final rank
2.9925
rank score
Inter norm
-0.896
normalised
Contacts
18
H-bonds 6
Strain ΔE
41.1 kcal/mol
SASA buried
81%
Lipo contact
65% BSA apolar/total
SASA unbound
709 Ų
Apolar buried
374 Ų

Interaction summary

HBD 2 HBA 2 HY 8 PI 3 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap9Native recall0.75
Jaccard0.43RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

1033 residues
Protein targetT17Atoms15160
Residues1033Chains2
Residue summaryVAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408

Receptor context

2 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 2 Excluded HETATM 0
Kept cofactors / ions
A:FAD501 B:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
396 -0.11056417959593262 -1.19533 -34.8331 9 17 0 0.00 0.00 - no Open
419 0.3271797508948459 -0.839972 -24.243 2 13 0 0.00 0.00 - no Open
480 0.4575261200251558 -0.989236 -25.5218 1 21 0 0.00 0.00 - no Open
388 1.3247621968802203 -0.97422 -27.5305 8 15 0 0.00 0.00 - no Open
429 1.5682838105176942 -0.894601 -23.8867 4 14 0 0.00 0.00 - no Open
452 1.7973468440035216 -0.986403 -22.7906 5 13 0 0.00 0.00 - no Open
450 1.8532223899879046 -0.707052 -19.9579 8 16 0 0.00 0.00 - no Open
442 2.056146307025179 -0.886151 -21.9132 8 18 0 0.00 0.00 - no Open
402 2.1313085350777627 -1.15443 -29.8157 14 17 0 0.00 0.00 - no Open
432 2.4339812204281435 -0.65996 -17.4537 6 10 0 0.00 0.00 - no Open
469 2.992470262134781 -0.896028 -22.0828 6 18 9 0.75 0.00 - no Current
408 3.228580280103112 -0.944403 -24.0255 6 19 0 0.00 0.00 - no Open
426 3.390641675980678 -0.781192 -18.2749 8 14 0 0.00 0.00 - no Open
398 3.736159295282282 -0.857475 -20.4087 13 15 0 0.00 0.00 - no Open
409 3.9602894299335802 -0.833689 -21.2615 10 15 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -22.083kcal/mol
Ligand efficiency (LE) -0.7361kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.101
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 458.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.59
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 41.07kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 52.05kcal/mol
Minimised FF energy 10.98kcal/mol

SASA & burial

✓ computed
SASA (unbound) 708.8Ų
Total solvent-accessible surface area of free ligand
BSA total 572.3Ų
Buried surface area upon binding
BSA apolar 373.8Ų
Hydrophobic contacts buried
BSA polar 198.5Ų
Polar contacts buried
Fraction buried 80.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 65.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6452.6Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2078.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)