FAIRMol

Z49606031

Pose ID 8742 Compound 988 Pose 612

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 Z49606031
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
29.6 kcal/mol
Protein clashes
0
Internal clashes
11
Native overlap
contact recall 0.74, Jaccard 0.64, H-bond role recall 0.57
Burial
74%
Hydrophobic fit
75%
Reason: 11 internal clashes
11 intramolecular clashes 37% of hydrophobic surface appears solvent-exposed (7/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.002 kcal/mol/HA) ✓ Good fit quality (FQ -9.46) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ High strain energy (29.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-28.050
kcal/mol
LE
-1.002
kcal/mol/HA
Fit Quality
-9.46
FQ (Leeson)
HAC
28
heavy atoms
MW
403
Da
LogP
2.04
cLogP
Final rank
3.2185
rank score
Inter norm
-1.045
normalised
Contacts
17
H-bonds 8
Strain ΔE
29.6 kcal/mol
SASA buried
74%
Lipo contact
75% BSA apolar/total
SASA unbound
623 Ų
Apolar buried
347 Ų

Interaction summary

HBD 1 HBA 5 HY 3 PI 3 CLASH 0

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
No clash · clashes detected for this pose.

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 overlap14Native recall0.74
Jaccard0.64RMSD-
HB strict6Strict recall0.67
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
608 0.28198169869884865 -0.85723 -23.1601 3 14 0 0.00 0.00 - no Open
591 0.9259440503290726 -1.08371 -28.7108 8 13 0 0.00 0.00 - no Open
606 1.8192507548808121 -1.04528 -29.0925 3 14 0 0.00 0.00 - no Open
613 2.2033316024264695 -0.9827 -35.251 7 16 1 0.05 0.14 - no Open
620 2.654583110640994 -0.867156 -29.8358 9 12 0 0.00 0.00 - no Open
610 2.660120191338177 -0.718352 -19.3503 8 10 0 0.00 0.00 - no Open
598 3.0805438009331887 -0.909389 -29.8286 6 18 0 0.00 0.00 - no Open
612 3.2185474535416136 -1.04492 -28.0502 8 17 14 0.74 0.57 - no Current
607 3.5827660316033643 -0.811178 -22.4444 7 13 0 0.00 0.00 - no Open
590 4.255366215778278 -1.056 -34.8672 6 13 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 -28.050kcal/mol
Ligand efficiency (LE) -1.0018kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.457
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.04
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 29.63kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 36.91kcal/mol
Minimised FF energy 7.28kcal/mol

SASA & burial

✓ computed
SASA (unbound) 623.5Ų
Total solvent-accessible surface area of free ligand
BSA total 461.4Ų
Buried surface area upon binding
BSA apolar 346.6Ų
Hydrophobic contacts buried
BSA polar 114.8Ų
Polar contacts buried
Fraction buried 74.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 75.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2526.2Ų
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 1385.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)