FAIRMol

Z56900576

Pose ID 8569 Compound 504 Pose 439

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 Z56900576
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
37.1 kcal/mol
Protein clashes
0
Internal clashes
6
Native overlap
contact recall 0.79, Jaccard 0.60, H-bond role recall 0.43
Burial
81%
Hydrophobic fit
77%
Reason: 6 internal clashes
6 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.994 kcal/mol/HA) ✓ Good fit quality (FQ -9.04) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Very high strain energy (37.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-24.852
kcal/mol
LE
-0.994
kcal/mol/HA
Fit Quality
-9.04
FQ (Leeson)
HAC
25
heavy atoms
MW
358
Da
LogP
0.98
cLogP
Strain ΔE
37.1 kcal/mol
SASA buried
81%
Lipo contact
77% BSA apolar/total
SASA unbound
581 Ų
Apolar buried
364 Ų

Interaction summary

HB 8 HY 4 PI 4 CLASH 0
Final rank1.505Score-24.852
Inter norm-1.181Intra norm0.187
Top1000noExcludedno
Contacts21H-bonds8
Artifact reasongeometry warning; 6 clashes; 1 protein clash; high strain Δ 37.1
Residues
ALA111 ALA67 ARG154 ARG277 ASN112 GLU274 GLY199 GLY235 GLY236 GLY237 GLY276 HIS197 LYS69 PHE170 PHE196 PHE238 PRO113 PRO275 SER200 TYR278 TYR389

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

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
Jaccard0.60RMSD-
HB strict5Strict recall0.56
HB same residue+role3HB role recall0.43
HB same residue4HB residue recall0.57

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
No clash · clashes detected for this pose.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
459 1.2720751774765935 -1.05921 -22.3772 5 17 0 0.00 0.00 - no Open
439 1.5054581612201845 -1.18078 -24.852 8 21 15 0.79 0.43 - no Current
503 2.8376502596628472 -1.16389 -30.1715 5 18 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 -24.852kcal/mol
Ligand efficiency (LE) -0.9941kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.037
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 358.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.98
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 37.13kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 65.92kcal/mol
Minimised FF energy 28.79kcal/mol

SASA & burial

✓ computed
SASA (unbound) 580.7Ų
Total solvent-accessible surface area of free ligand
BSA total 471.6Ų
Buried surface area upon binding
BSA apolar 363.8Ų
Hydrophobic contacts buried
BSA polar 107.8Ų
Polar contacts buried
Fraction buried 81.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2523.8Ų
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 1386.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)