FAIRMol

OHD_MAC_34

Pose ID 8460 Compound 657 Pose 330

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_MAC_34
PDB1F3T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
36.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.79, Jaccard 0.62, H-bond role recall 0.71
Burial
78%
Hydrophobic fit
81%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.670 kcal/mol/HA) ✓ Good fit quality (FQ -6.40) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ Very high strain energy (36.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (15)
Score
-19.441
kcal/mol
LE
-0.670
kcal/mol/HA
Fit Quality
-6.40
FQ (Leeson)
HAC
29
heavy atoms
MW
408
Da
LogP
3.67
cLogP
Strain ΔE
36.8 kcal/mol
SASA buried
78%
Lipo contact
81% BSA apolar/total
SASA unbound
657 Ų
Apolar buried
417 Ų

Interaction summary

HB 9 HY 11 PI 5 CLASH 1

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 rank4.487Score-19.441
Inter norm-1.100Intra norm0.429
Top1000noExcludedno
Contacts20H-bonds9
Artifact reasongeometry warning; 15 clashes; 3 protein clashes; high strain Δ 36.8
Residues
ALA67 ARG277 ASN327 ASP332 GLU274 GLY199 GLY236 GLY237 GLY276 GLY393 HIS197 HIS333 LYS69 PHE238 PRO275 SER200 TYR278 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 overlap15Native recall0.79
Jaccard0.62RMSD-
HB strict5Strict recall0.56
HB same residue+role5HB role recall0.71
HB same residue5HB residue recall0.71

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
323 0.6813957279927266 -1.06167 -19.4935 10 12 0 0.00 0.00 - no Open
307 1.0464589408462037 -1.07635 -21.6753 9 22 0 0.00 0.00 - no Open
371 2.1930507818984033 -0.719578 -20.925 7 16 0 0.00 0.00 - no Open
440 3.156565364820583 -0.91643 -18.9903 5 16 0 0.00 0.00 - no Open
420 3.8152621832018965 -0.931014 -26.9895 5 14 0 0.00 0.00 - no Open
467 3.950885639121711 -0.822251 -21.0851 10 15 0 0.00 0.00 - no Open
361 4.047118682130805 -1.0099 -21.3506 14 16 0 0.00 0.00 - no Open
403 4.380419347645987 -0.960354 -19.9918 7 17 0 0.00 0.00 - no Open
330 4.487089281573849 -1.0998 -19.4414 9 20 15 0.79 0.71 - no Current
438 5.716213984919554 -0.923264 -19.2446 7 19 0 0.00 0.00 - no Open
365 5.933590350616897 -1.0124 -22.3953 7 16 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 -19.441kcal/mol
Ligand efficiency (LE) -0.6704kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.399
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 407.8Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.67
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 36.84kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 94.12kcal/mol
Minimised FF energy 57.28kcal/mol

SASA & burial

✓ computed
SASA (unbound) 656.7Ų
Total solvent-accessible surface area of free ligand
BSA total 515.2Ų
Buried surface area upon binding
BSA apolar 417.3Ų
Hydrophobic contacts buried
BSA polar 97.9Ų
Polar contacts buried
Fraction buried 78.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2572.1Ų
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 1423.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)