FAIRMol

OHD_TB2020_17

Pose ID 8152 Compound 2601 Pose 22

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
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand OHD_TB2020_17
PDB1F3T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
46.5 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 0.95, Jaccard 0.75, H-bond role recall 0.57
Burial
79%
Hydrophobic fit
80%
Reason: 7 internal clashes, strain 46.5 kcal/mol
strain ΔE 46.5 kcal/mol 7 protein-contact clashes 7 intramolecular 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 High Ames Clear DILI Risk
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.711 kcal/mol/HA) ✓ Good fit quality (FQ -7.17) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Extreme strain energy (46.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)
Score
-24.897
kcal/mol
LE
-0.711
kcal/mol/HA
Fit Quality
-7.17
FQ (Leeson)
HAC
35
heavy atoms
MW
496
Da
LogP
4.39
cLogP
Final rank
6.1229
rank score
Inter norm
-0.809
normalised
Contacts
23
H-bonds 11
Strain ΔE
46.5 kcal/mol
SASA buried
79%
Lipo contact
80% BSA apolar/total
SASA unbound
836 Ų
Apolar buried
527 Ų

Interaction summary

HBD 3 HBA 5 HY 5 PI 3 CLASH 7

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 6.

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: permissive.
Name1F3TContacts19
PoseOpen native poseHB0
IFP residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR331 TYR389
Current overlap18Native recall0.95
Jaccard0.75RMSD-
HB strict5Strict recall0.56
HB same residue+role4HB role recall0.57
HB same residue4HB residue recall0.57

Protein summary

411 residues
Protein targetT13Atoms6340
Residues411Chains1
Residue summaryVAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
45 2.074274147786298 -0.661547 -18.9256 2 20 0 0.00 0.00 - no Open
38 3.6771447614901684 -0.781966 -28.0582 12 15 0 0.00 0.00 - no Open
22 6.122942433269545 -0.809266 -24.8972 11 23 18 0.95 0.57 - no Current

Molecular metrics

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

Scoring & efficiency
Docking score -24.897kcal/mol
Ligand efficiency (LE) -0.7113kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.175
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 35HA

Physicochemical properties
Molecular weight 495.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.39
Lipinski: ≤ 5
Rotatable bonds 11

Conformational strain (MMFF94s)
Strain energy (ΔE) 46.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 90.77kcal/mol
Minimised FF energy 44.30kcal/mol

SASA & burial

✓ computed
SASA (unbound) 835.6Ų
Total solvent-accessible surface area of free ligand
BSA total 659.3Ų
Buried surface area upon binding
BSA apolar 526.8Ų
Hydrophobic contacts buried
BSA polar 132.6Ų
Polar contacts buried
Fraction buried 78.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2732.5Ų
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 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1407.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)