FAIRMol

OHD_TB2021_21

Pose ID 8157 Compound 4071 Pose 27

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_TB2021_21
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
71.9 kcal/mol
Protein clashes
8
Internal clashes
8
Native overlap
contact recall 0.89, Jaccard 0.81, H-bond role recall 0.57
Burial
78%
Hydrophobic fit
74%
Reason: 8 internal clashes, strain 71.9 kcal/mol
strain ΔE 71.9 kcal/mol 8 protein-contact clashes 8 intramolecular clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Low
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.810 kcal/mol/HA) ✓ Good fit quality (FQ -7.65) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Extreme strain energy (71.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-22.681
kcal/mol
LE
-0.810
kcal/mol/HA
Fit Quality
-7.65
FQ (Leeson)
HAC
28
heavy atoms
MW
406
Da
LogP
1.95
cLogP
Final rank
5.3551
rank score
Inter norm
-0.982
normalised
Contacts
19
H-bonds 9
Strain ΔE
71.9 kcal/mol
SASA buried
78%
Lipo contact
74% BSA apolar/total
SASA unbound
647 Ų
Apolar buried
373 Ų

Interaction summary

HBD 2 HBA 5 HY 3 PI 3 CLASH 8

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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: strict.
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 overlap17Native recall0.89
Jaccard0.81RMSD-
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
26 3.6484606353219524 -1.28294 -29.9802 10 24 0 0.00 0.00 - no Open
27 5.3551198480268685 -0.981985 -22.6807 9 19 17 0.89 0.57 - no Current
48 5.512523510317045 -0.96805 -25.7853 13 17 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 -22.681kcal/mol
Ligand efficiency (LE) -0.8100kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.647
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 406.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.95
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 71.86kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 52.57kcal/mol
Minimised FF energy -19.28kcal/mol

SASA & burial

✓ computed
SASA (unbound) 647.2Ų
Total solvent-accessible surface area of free ligand
BSA total 502.8Ų
Buried surface area upon binding
BSA apolar 372.8Ų
Hydrophobic contacts buried
BSA polar 130.0Ų
Polar contacts buried
Fraction buried 77.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2560.3Ų
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 1390.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)