FAIRMol

Z2940609369

Pose ID 8667 Compound 1251 Pose 537

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 Z2940609369
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 high Native strong SASA done
Strain ΔE
5.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.74, Jaccard 0.70, H-bond role recall 0.71
Burial
78%
Hydrophobic fit
77%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Low conformational strain (5.8 kcal/mol) ✓ Excellent LE (-1.432 kcal/mol/HA) ✓ Good fit quality (FQ -11.98) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Geometry warnings ✗ Protein-contact clashes (9) ✗ Internal clashes (9)
Score
-28.639
kcal/mol
LE
-1.432
kcal/mol/HA
Fit Quality
-11.98
FQ (Leeson)
HAC
20
heavy atoms
MW
271
Da
LogP
2.23
cLogP
Strain ΔE
5.8 kcal/mol
SASA buried
78%
Lipo contact
77% BSA apolar/total
SASA unbound
500 Ų
Apolar buried
302 Ų

Interaction summary

HB 9 HY 5 PI 2 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 rank0.900Score-28.639
Inter norm-1.580Intra norm0.148
Top1000noExcludedno
Contacts15H-bonds9
Artifact reasongeometry warning; 9 clashes; 9 protein contact clashes
Residues
ALA67 ARG277 ASP332 GLU274 GLY236 GLY237 GLY276 HIS197 HIS333 LYS69 PHE238 PRO275 SER200 TYR331 TYR389

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
Jaccard0.70RMSD-
HB strict4Strict recall0.44
HB same residue+role5HB role recall0.71
HB same residue6HB residue recall0.86

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
521 -0.07895923437601685 -1.64823 -27.6509 6 17 0 0.00 0.00 - no Open
521 0.6898490708952878 -1.39958 -22.7449 9 14 0 0.00 0.00 - no Open
528 0.7995282429380937 -1.68304 -30.0302 7 11 0 0.00 0.00 - no Open
537 0.9000688127635621 -1.5798 -28.6387 9 15 14 0.74 0.71 - no Current
555 1.898156266383085 -1.19422 -20.9939 8 14 0 0.00 0.00 - no Open
552 2.174966198704028 -1.36094 -22.3096 6 15 0 0.00 0.00 - no Open
537 3.7603426496280146 -1.12156 -19.3209 5 12 0 0.00 0.00 - no Open
530 3.9775243006343235 -1.42387 -26.5144 9 19 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 -28.639kcal/mol
Ligand efficiency (LE) -1.4319kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.983
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 20HA

Physicochemical properties
Molecular weight 271.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.23
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 5.84kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 69.63kcal/mol
Minimised FF energy 63.79kcal/mol

SASA & burial

✓ computed
SASA (unbound) 499.6Ų
Total solvent-accessible surface area of free ligand
BSA total 391.1Ų
Buried surface area upon binding
BSA apolar 301.6Ų
Hydrophobic contacts buried
BSA polar 89.6Ų
Polar contacts buried
Fraction buried 78.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2469.7Ų
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 1390.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)