FAIRMol

NMT-TY0958

Pose ID 5053 Compound 18 Pose 312

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
T08
T. brucei PTR1 T. brucei
Ligand NMT-TY0958
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
Weak or marginal quality
Binding strong Geometry high Native strong SASA done
Strain ΔE
22.7 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.68, Jaccard 0.65, H-bond role recall 0.40
Burial
89%
Hydrophobic fit
75%
Reason: no major geometry red flags detected
1 protein-contact 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 (-1.198 kcal/mol/HA) ✓ Good fit quality (FQ -11.44) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ High strain energy (22.7 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Many internal clashes (12)
Score
-34.741
kcal/mol
LE
-1.198
kcal/mol/HA
Fit Quality
-11.44
FQ (Leeson)
HAC
29
heavy atoms
MW
432
Da
LogP
2.46
cLogP
Strain ΔE
22.7 kcal/mol
SASA buried
89%
Lipo contact
75% BSA apolar/total
SASA unbound
685 Ų
Apolar buried
460 Ų

Interaction summary

HB 12 HY 23 PI 2 CLASH 2 ⚠ Exposure 36%

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
⚠️Partial hydrophobic solvent exposure
37% of hydrophobic surface appears solvent-exposed (7/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19 Buried (contacted) 12 Exposed 7 LogP 2.46 H-bonds 12
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank0.484Score-34.741
Inter norm-1.249Intra norm0.051
Top1000noExcludedno
Contacts14H-bonds12
Artifact reasongeometry warning; 12 clashes; 2 protein contact clashes; 5 cofactor-context clashes; moderate strain Δ 22.7
Residues
ARG14 ASP161 CYS168 LEU208 LEU209 LYS13 MET213 NAP301 PHE97 PRO210 SER95 TRP221 TYR174 VAL206

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 overlap13Native recall0.68
Jaccard0.65RMSD-
HB strict3Strict recall0.50
HB same residue+role2HB role recall0.40
HB same residue3HB residue recall0.60

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
404 0.35774331463703657 -0.999567 -29.3052 6 18 0 0.00 0.00 - no Open
312 0.48352440256161 -1.24923 -34.7407 12 14 13 0.68 0.40 - no Current
336 1.4675637408200402 -0.875222 -17.7108 6 21 0 0.00 0.00 - no Open
348 1.9597176038158632 -0.764019 -22.0844 8 14 0 0.00 0.00 - no Open
390 2.085703360804628 -0.981011 -28.2007 5 17 0 0.00 0.00 - no Open
333 2.2998264280481555 -1.0763 -32.068 10 17 0 0.00 0.00 - no Open
290 2.597929268126482 -1.10452 -30.118 8 21 0 0.00 0.00 - no Open
335 2.684907728138777 -0.777837 -18.265 7 18 0 0.00 0.00 - no Open
299 3.641447029952177 -1.09529 -33.2465 10 17 0 0.00 0.00 - no Open
452 3.6964323676775086 -0.903139 -26.2642 8 18 0 0.00 0.00 - no Open
325 4.609247539147728 -1.11712 -31.2798 14 27 0 0.00 0.00 - no Open
378 4.916801977951926 -0.84486 -21.716 6 21 0 0.00 0.00 - no Open
331 4.967104415660727 -0.967475 -29.398 11 16 0 0.00 0.00 - no Open
285 5.22879534295586 -0.923838 -24.6534 13 14 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 -34.741kcal/mol
Ligand efficiency (LE) -1.1980kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.435
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 431.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.46
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -52.75kcal/mol
Minimised FF energy -75.43kcal/mol

SASA & burial

✓ computed
SASA (unbound) 685.1Ų
Total solvent-accessible surface area of free ligand
BSA total 612.2Ų
Buried surface area upon binding
BSA apolar 460.0Ų
Hydrophobic contacts buried
BSA polar 152.2Ų
Polar contacts buried
Fraction buried 89.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 75.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1650.0Ų
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 929.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)