FAIRMol

Z104497306

Pose ID 8602 Compound 2679 Pose 472

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 Z104497306
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
22.1 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.79, Jaccard 0.62, H-bond role recall 0.43
Burial
94%
Hydrophobic fit
67%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.409 kcal/mol/HA) ✓ Good fit quality (FQ -11.29) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (67%) ✗ High strain energy (22.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-25.354
kcal/mol
LE
-1.409
kcal/mol/HA
Fit Quality
-11.29
FQ (Leeson)
HAC
18
heavy atoms
MW
265
Da
LogP
0.45
cLogP
Final rank
4.1083
rank score
Inter norm
-1.928
normalised
Contacts
20
H-bonds 12
Strain ΔE
22.1 kcal/mol
SASA buried
94%
Lipo contact
67% BSA apolar/total
SASA unbound
482 Ų
Apolar buried
302 Ų

Interaction summary

HBD 2 HBA 5 PC 1 HY 4 PI 2 CLASH 6

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.

PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.

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 overlap15Native recall0.79
Jaccard0.62RMSD-
HB strict5Strict recall0.56
HB same residue+role3HB role recall0.43
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
454 -0.21749554397758344 -1.75178 -24.6391 12 16 0 0.00 0.00 - no Open
480 2.44337014472352 -1.42438 -24.2473 5 14 0 0.00 0.00 - no Open
465 2.7704179659118466 -1.51719 -23.8017 14 18 0 0.00 0.00 - no Open
466 4.00752394528947 -1.47405 -18.6377 16 17 0 0.00 0.00 - no Open
472 4.108278491893934 -1.92763 -25.3542 12 20 15 0.79 0.43 - 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 -25.354kcal/mol
Ligand efficiency (LE) -1.4086kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.289
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 18HA

Physicochemical properties
Molecular weight 265.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.45
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.11kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -168.48kcal/mol
Minimised FF energy -190.59kcal/mol

SASA & burial

✓ computed
SASA (unbound) 481.9Ų
Total solvent-accessible surface area of free ligand
BSA total 451.3Ų
Buried surface area upon binding
BSA apolar 301.8Ų
Hydrophobic contacts buried
BSA polar 149.5Ų
Polar contacts buried
Fraction buried 93.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 66.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2410.7Ų
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 1382.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)