FAIRMol

Z49891479

Pose ID 5189 Compound 2357 Pose 448

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
T08
T. brucei PTR1 T. brucei
Ligand Z49891479
PDB6RX6↗

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
22.9 kcal/mol
Protein clashes
6
Internal clashes
7
Native overlap
contact recall 0.58, Jaccard 0.46, H-bond role recall 0.00
Burial
96%
Hydrophobic fit
76%
Reason: 7 internal clashes
6 protein-contact clashes 7 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.104 kcal/mol/HA) ✓ Good fit quality (FQ -9.89) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (96% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ High strain energy (22.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-26.487
kcal/mol
LE
-1.104
kcal/mol/HA
Fit Quality
-9.89
FQ (Leeson)
HAC
24
heavy atoms
MW
340
Da
LogP
3.34
cLogP
Strain ΔE
22.9 kcal/mol
SASA buried
96%
Lipo contact
76% BSA apolar/total
SASA unbound
588 Ų
Apolar buried
429 Ų

Interaction summary

HB 6 HY 24 PI 3 CLASH 7

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 rank2.101Score-26.487
Inter norm-1.322Intra norm0.218
Top1000noExcludedno
Contacts16H-bonds6
Artifact reasongeometry warning; 7 clashes; 1 protein clash; 1 severe cofactor-context clash; moderate strain Δ 22.9
Residues
ARG14 ASN175 ASP161 CYS168 GLN166 LEU208 LEU209 MET163 NAP301 PHE171 PHE97 PRO167 PRO210 SER95 TYR174 VAL164

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameTbPTR1_cW_6RX6_ReadyContacts19
PoseOpen native poseHB0
IFP residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS178 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER207 SER95 TRP221 TYR174 TYR98 VAL206
Current overlap11Native recall0.58
Jaccard0.46RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue1HB residue recall0.20

Protein summary

258 residues
Protein targetT08Atoms3881
Residues258Chains2
Residue summaryLEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:NAP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
427 0.1637210485937671 -0.972095 -17.9721 1 14 0 0.00 0.00 - no Open
448 2.1011499600434522 -1.32189 -26.4874 6 16 11 0.58 0.00 - no Current
432 3.481521830671832 -1.14179 -26.8947 7 17 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 -26.487kcal/mol
Ligand efficiency (LE) -1.1036kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.891
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 340.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.34
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 69.78kcal/mol
Minimised FF energy 46.89kcal/mol

SASA & burial

✓ computed
SASA (unbound) 588.2Ų
Total solvent-accessible surface area of free ligand
BSA total 561.6Ų
Buried surface area upon binding
BSA apolar 428.9Ų
Hydrophobic contacts buried
BSA polar 132.6Ų
Polar contacts buried
Fraction buried 95.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1564.6Ų
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 2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 934.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)