FAIRMol

OHD_TB2023_5

Pose ID 8171 Compound 3739 Pose 41

DB SELECTIONDocking 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_TB2023_5
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
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
38.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.63, Jaccard 0.40, H-bond role recall 0.00
Burial
81%
Hydrophobic fit
92%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.950 kcal/mol/HA) ✓ Good fit quality (FQ -9.58) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (92%) ✗ Very high strain energy (38.6 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (5) ✗ Many internal clashes (20)
Score
-33.251
kcal/mol
LE
-0.950
kcal/mol/HA
Fit Quality
-9.58
FQ (Leeson)
HAC
35
heavy atoms
MW
505
Da
LogP
3.69
cLogP
Strain ΔE
38.6 kcal/mol
SASA buried
81%
Lipo contact
92% BSA apolar/total
SASA unbound
786 Ų
Apolar buried
588 Ų

Interaction summary

HB 6 HY 20 PI 4 CLASH 3

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

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

HY · Hydrophobic contacts

CLASH · Clashes
Final rank2.159Score-33.251
Inter norm-0.894Intra norm-0.056
Top1000noExcludedno
Contacts23H-bonds6
Artifact reasongeometry warning; 20 clashes; 5 protein contact clashes; high strain Δ 38.6
Residues
ALA111 ALA67 ARG154 ARG277 ASN112 ASN327 ASP233 ASP332 ASP88 CYS328 GLU274 GLY235 GLY236 GLY393 HIS197 LYS69 PHE196 PRO113 SER195 THR132 TYR331 TYR389 VAL392

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 overlap12Native recall0.63
Jaccard0.40RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue2HB residue recall0.29

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
41 2.1594928344831876 -0.893707 -33.2508 6 23 12 0.63 0.00 - no Current
63 2.823587428131222 -0.790606 -29.6579 4 21 0 0.00 0.00 - no Open
77 3.3076659022431727 -0.647397 -27.3866 6 14 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 -33.251kcal/mol
Ligand efficiency (LE) -0.9500kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.582
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 35HA

Physicochemical properties
Molecular weight 505.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.69
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 38.64kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 132.97kcal/mol
Minimised FF energy 94.32kcal/mol

SASA & burial

✓ computed
SASA (unbound) 785.6Ų
Total solvent-accessible surface area of free ligand
BSA total 638.8Ų
Buried surface area upon binding
BSA apolar 588.4Ų
Hydrophobic contacts buried
BSA polar 50.5Ų
Polar contacts buried
Fraction buried 81.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 92.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2756.2Ų
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 1411.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)